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111  structures 7268  species 0  interactions 62462  sequences 282  architectures

Family: Usp (PF00582)

Summary: Universal stress protein family

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Universal stress protein Edit Wikipedia article

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Universal Stress Protein A
UspA protein structure from Lactobacillus plantarum
UspA protein structure from Lactobacillus plantarum [1]
Pfam clanHUP

The universal stress protein (USP) domain is a superfamily of conserved genes which can be found in bacteria, archaea, fungi, protozoa and plants [2]. Proteins containing the domain are induced by a plethora of environmental stressors. These conditions include nutrient starvation, drought, extreme temperatures, high salinity, and the presence of uncouplers, antibiotics and metals. [2].

In the presence of these stressors, Usp genes are upregulated resulting in large quantities of their subsequent proteins being produced throughout the cell. The over production of USP domain containing genes allows the organisms to better cope with a varied range of environmental stresses via the action of a number of largely unknown mechanisms. Once stimulated, the USPs will alter the expression of a variety of different genes involved in many different cellular processes. The end result is increased resistance to the stressful condition making this a type of biological defence mechanism. Organisms have many thousands of copies of USP domains within as many genes. However, it is not often known in detail the differences in mechanisms of induction or protection [3]


The protein structure of a Universal Stress Protein found in Haemophylus influenzae [4]

The primary function of this superfamily of genetic domains is to protect the organism during times of environmental stress. Environmental stress, as previously explained, comes in a number of forms. Exposure to a harmful substance or condition, such as UV light, may induce genes containing the USP domain in order to protect the DNA and more generally the cell from further damage [2]. A key example can be found during periods of starvation. In these instances, the USP genes upregulated will often arrest cell growth and in the case of some bacteria, promote a shift to differential metabolic mechanisms which are favourable in conditions of sparse nutrients [2].

Recent research also suggests proteins containing this domain have functions beyond the realms of dealing with environmental stresses [5]. Nachin et al demonstrated in Escherichia coli that USPs are involved in actions such as adhesion and motility. The researchers, through means of "knocking out" USP genes known as UspE and UspC, saw results suggesting an inability to swim and completely lack of motility, respectively. Conversely, mutants for genes UspF and UspG were shown to have enhanced swimming abilities. Therefore, mobility is affected both positively and negatively USPs within E. coli. This demonstrates USPs influence throughout the cell could be widespread for a number of reasons.

Additionally, in Halmonas elongate, there is a USP called TeaD has been described as a key regulator in the transport of Ectoine across the cell membrane [6]. This demonstrates how versatile USPs can be. Their function, while primarily encompasses increasing survival during stressful conditions, is not always limited to this.


The ubiquitous nature of these proteins suggests the domain evolved in an ancestral species as well as highlighting the clear biological significance these proteins have in order to still be present the three domains of life. It has been suggested that the USP A domain was part of an ancient protein family. This is due to the similarity in structure between many distantly related organisms [7].Aravind et al confirmed these ideas with extensive evolutionary analysis. Aravind suggested that these proteins were part of a much larger protein structural family which was present and diversified in our last universal common ancestor for all extant life [7]. The original function has been suggested to be a nucleotide binding domain which was implicated in signal transduction [8]


As the USP domain is widespread across many organisms, there is great diversity in the structures of these proteins. For Haemophilus influenzae, its UspA resides in the cytoplasm. The protein forms an asymmetric dimer with characteristic alpha and beta fold structures. There are differences among different bacteria in areas such as ATP binding sites [2]. In this case, UspA does not have ATP binding activity. Generally, USPs form dimers and have domains for nucleotide binding activity. However, as it is such a diverse group, often with little known about the exact structure, it’s not possible to comment on each USP. In addition to this, UspA may reside in different areas of the cell. For example, in this case it was in the cytoplasm but for others, it may be in the cell membrane. [9]


Much of the research into USP is done on bacteria, specifically E. coli (Strain K-12). Consequently, much is known about the USP domains in bacteria. In E. coli there are six families of USP domains which are present in more than 1000 different proteins [10]. The six families are Usp A, -C, -D, -E, -F and –G which are triggered by differing environmental insults and often act via varying mechanisms. [10]

UspA is the most commonly studied USP due to its widespread presence within bacterial genomes. UspA is especially implicated in the resistance of a huge number of stressors most notably tetracycline exposure and high temperatures, with the exception of not forming a response to cold shock. It is thought UspA is especially important to the recovery of E. coli following starvation of nutrients [2]. UspA during normal growth conditions does not seem to influence gene expression. However, during stressful conditions such as carbon starvation, UspA has been shown to have a global influence on gene expression. A proposed mechanism for such a change in gene expression is that UspA has been suggested to bind to DNA. When UspA is mutated, E. coli becomes far more vulnerable UV induced DNA damage.[11]. It’s important to note the USP responses are independent of many other stress responses seen in bacteria such as rpoS. [12].

This schematic shows a generalised bacterial response to an environmental stress. In this case, it depicts increased levels of Nitric Oxide which stimulates Usp gene transcription. This results in an anti-stress response from the cell which may or may not include the responses listed within the diagram.[13]

The induction of USP proteins have also been implicated in transitions not only in metabolism or growth but in changes in the colonies' entire phenotype. Bacterial colonies can produce formations known as biofilms. Zhang and colleagues demonstrated that USPs may be involed in the promotion of intertidal biofilms [13]. They observed that during stressful conditions involving metal ions and oxidative stresses that the biofilm phenotype would form. Upon analysis of these biofilms, it could be seen that there was a greatly upregulated level of UspA which Zhang suggests, may be involved with induction of biofilm formation. It is thought UspA may be involved in signalling processes which will upregulate genes involved with biofilm production.[12]. With findings such as these, it's beginning to be accepted that USPs are acting using an extremely wide range of mechanisms to ensure cell survival.


In bacteria, the USP genes can be regulated by sigma factors within RNA polymerases. This includes sigma factor σ70 which through binding to a single promoter region, upregulates the transcription of UspA in bacteria. The genes are regulated in a monocistronic fashion. [14]. Additionally, UspA, UspC, UspD and UspE are over induced during stationary phase through regulation of RecA. RecA is known for its involvement in the repair of DNA via homologous recombination following damage. Consequently, the four Usp domain genes are thought to be mediating the management or protection of DNA [15]. Whatever the mechanism exhibited by the proteins, one thing which can be concluded is that USP domains are crucial for survival of many bacterial species. Gomes et al found that UspA deletions in Listeria severely impaired survival as well as listeria’s stress response by in vitro and in vivo [16].

USP domain genes are regulated by a number of proteins involved with growth, DNA repair and cell division. Notable positive regulation occurs via the action of ppGpp, RecA and FtsZ dependent regulatory pathways. USP domain genes are also under the negative control of FadR. [17]


Plants contain many hundreds of USP domains and genes. These genes are notably induced by environmental stresses such as drought. When a lack of hydration occurs, biochemical changes induced by the actions of USPs ensue. In response to drought, there is a reduction in photosynthetic carbon production as well as a reduction in energy metabolism[18]. These actions are suggested to occur due to their implications in increasing energy conservation. Water limiting conditions are a common environmental pressure which plants will need to cope with on a regular basis, depending on their habitat. These resistant phenotypes will have an increased survival as they allow the plant to conserve energy in times of restricted water which is key to glucose production through photosynthesis [18].

Clinical significance


Mycobacterium tuberculosis, the infectious agent responsible for Tuberculosis (TB), persists within an estimated two billion people. TB is known for its ability to transition into a latent state whereby there is slow growth but high persistence within the mammalian host in structures known as granulomas [19]. These granuloma structures are made up of various cellular materials and immune cells. These include macrophages, neutrophils, cellulose and fats. It has long been proposed that USPs play a significant role in the persistence of TB within the human host. This is due to observations of elevated Usp genes within M. tuberculosis in the latent granuloma stage of the infection [20].

There are eight types of USPs within M. tuberculosis, all of which have an ATP binding domain. It has been found that within M. tuberculosis, these USPs are regulated by FtsK and FadR [21]. One recent finding shows that the induction of USPs within M. tuberculosis results in USP binding activity with intracellular cAMP which has indirect implications on transcription within the bacteria [22].

Some of M. tuberculosis' USPs are suggested to be induced by the hypoxic conditions found within the granuloma. Specifically, Rv2623, a type of USP in M. tuberculosis, is induced by the presence of nitric oxide, reactive oxygen species and a downshift in pH. All of these conditions are suggested to be produced by the actions of macrophages which are particularly prevalent within the granuloma structures that are characteristic of TB latent infections. [20]. These conditions have been found to upregulate a particular USP gene called rv2623, as well as an additional 50 genes involved in long term persistence in the mammalian host. It was suggested this USP gene was involved in inducing the latent response within the mammalian host. This stage of the infection is currently chronic with no effective treatments. This makes these kinds of findings extremely valauble.

Rv2623 has an ATP binding domain which if knocked out results in a hyper-virulent form of the bacteria. [21]. Understanding these processes aids researchers in their quest to provide effective treatment for those suffering from TB. Rv2623 is also a key biomarker aiding the diagnostic process for TB. Therefore these USP genes could be crucial for the long term survival of the bacteria meaning that there may be potential therapeutic avenues of research to explore in treating latent TB. [23]. This comes at a time whereby TB kills many thousands of people a day and is becoming increasing problematic to treat with the rise of multi-drug-resistant TB.


Similarly, USPs are crucial for the survival of Salmonella, the causative agent in Salmonellosis. In developing countries, food poisoning of this kind is a potentially life-threatening condition. The USPs have influence in growth arrest, stress responses and virulence [24]. UspA is induced by metabolic, oxidative and temperature related stress. In these conditions UspA is over produced through the transcriptional regulation by ppGpp and RecA. These responses have been suggested to be involved in the protection of DNA. As a result, UspA aids Salmonella to resist stressors produced by the mammalian immune system assisting in survival and hence, pathogenicity [24]. When UspA is inactivated in Salmonella, the mutants die prematurely, demonstrating how crucial these proteins are to survival and persistence. Again, understanding these processes may aid researchers in developing effective drugs to treat these infections [24].


  1. ^ Tan K; et al. "The crystal structure of an universal stress protein UspA family protein from Lactobacillus plantarum WCFS1". To be published. {{cite journal}}: Explicit use of et al. in: |author= (help); Text "doi: 10.2210/pdb3fg9/pdb" ignored (help).
  2. ^ a b c d e f Siegele DA; et al. (2005). "Universal Stress Proteins in Escherichia coli". Journal of Bacteria. 187: 6253–6254. {{cite journal}}: Explicit use of et al. in: |author= (help).
  3. ^ Tkaczuk KL; et al. (2013). "Structural and functional insight into the universal stress protein family". Evolutionary Applications. 6: 434–449. {{cite journal}}: Explicit use of et al. in: |author= (help); Text "doi: 10.1111/eva.12057" ignored (help).
  4. ^ Sousa MC (2001). "Structure of Haemophylus influenzae Universal Stress Protein At 1.85A Resolution". Structure. 9: 1135–1141. {{cite journal}}: Text "doi:10.2210/pdb1jmv/pdb" ignored (help).
  5. ^ Nachin L; et al. (2005). "Differential Roles of the Universal Stress Proteins of Escherichia coli in Oxidative Stress Resistance, Adhesion, and Motility". Journal of Bacteriology. 187: 6265–6272. {{cite journal}}: Explicit use of et al. in: |author= (help); Text "doi:10.1128/JB.187.18.6265–6272.2005" ignored (help); line feed character in |title= at position 72 (help).
  6. ^ Schweikhard ES; et al. (2010). "Structure and function of the universal stress protein TeaD and its role in regulating the ectoine transporter TeaABC of Halomonas elongata DSM 2581(T)". Biochemistry. 49: 2194–2204. {{cite journal}}: Explicit use of et al. in: |author= (help); Text "doi:10.1021/bi9017522" ignored (help).
  7. ^ a b Aravind L; et al. (2002). "Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA". Protein. 48: 1–14. {{cite journal}}: Explicit use of et al. in: |author= (help).
  8. ^ Becker JD (2001). "The nodulin vfENOD18 is an ATP-binding protein in infected cells of Vicia faba L. nodules". Plant Mol Biol. 47: 749–759..
  9. ^ Sousa MC (2001). "Structure of the universal stress protein of Haemophilus influenzae". Bichemical Sciences. 9: 1135–1141.
  10. ^ a b Bateman A (2004). "The Pfam protein families database". Nucleic Acid Research. 32: 138–141. doi:10.1093/nar/gkh121.
  11. ^ O'Toole R (2003). "Universal stress proteins and Mycobacterium tuberculosis". Research in Microbiology. 154: 387–392. doi:10.1016/S0923-2508(03)00081-0.
  12. ^ a b Gustavsson N (2002). "The universal stress protein paralogues of Escherichia coli are co-ordinately regulated and co-operate in the defence against DNA damage". Molecular Microbiology. 43: 107–117. doi:10.1046/j.1365-2958.2002.02720.x.
  13. ^ a b Zhang W (2013). "Adaptation of intertidal biofilm communities is driven by metal ion and oxidative stresses". Scientific Reports. 3: 3180. doi:10.1038/srep03180.
  14. ^ Kvint K (2013). "The bacterial universal stress protein: function and regulation". Curr Opin Microbiol. 6: 140–145.
  15. ^ Diez A (2002). "The universal stress protein A of Escherichia coli is required for resistance to DNA damaging agents and is regulated by a RecA/FtsK-dependent regulatory pathway". Molecular Microbiology. 36: 1494–1503.
  16. ^ Gomes CS (2011). "Universal Stress Proteins Are Important for Oxidative and Acid Stress Resistance and Growth of Listeria monocytogenes EGD-e In Vitro and In Vivo". PLOS. 6: e24965. doi:10.1371/journal.pone.0024965.
  17. ^ "The Universal Stress Protein A"". Uniprot. 25-03-2015. Retrieved 25-03-2015. {{cite web}}: Check date values in: |access-date= and |date= (help)
  18. ^ a b Isokpehi RD (2011). "Identification of drought-responsive universal stress proteins in viridiplantae". bioinform Biol Insights. 5: 41–58. doi:10.4137/BBI.S6061.
  19. ^ Ramakrishnan L (2012). "Revisiting the role of the granuloma in tuberculosis". Nature Reviews. 12: 352–366. doi:doi:10.1038/nri3211. {{cite journal}}: Check |doi= value (help)
  20. ^ a b O'Toole R (2003). "Universal stress proteins and Mycobacterium tuberculosis". Research in Microbiology. 6: 387–392.
  21. ^ a b Drumm JE (2009). "Mycobacterium tuberculosis universal stress protein Rv2623 regulates bacillary growth by ATP-Binding: requirement for establishing chronic persistent infection". PloS Pathog. 5: e1000460. doi:10.1371/journal.ppat.1000460. {{cite journal}}: Check |doi= value (help)
  22. ^ Banerjee A (2015). "A Universal Stress Protein (USP) in Mycobacteria binds cAMP". The Journal of Biological Chemistry. 12: 1–28. doi:10.1074/jbc.M115.644856.
  23. ^ Hingley-Wilson SM (2010). "Individual Mycobacterium tuberculosis universal stress protein homologues are dispensable in vitro". Tuberculosis. 90: 236–244. doi:10.1016/
  24. ^ a b c Liu WT (2007). "Role of the universal stress protein UspA of Salmonella in growth arrest, stress and virulence". Microbial Pathogenesis. 42: 2–10.

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Universal stress protein family Provide feedback

The universal stress protein UspA P28242 [1] is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA [3] reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP [2] though UspA lacks ATP-binding activity.

Literature references

  1. Nystrom T, Neidhardt FC; , Mol Microbiol 1994;11:537-544.: Expression and role of the universal stress protein, UspA, of Escherichia coli during growth arrest. PUBMED:8152377 EPMC:8152377

  2. Zarembinski TI, Hung LW, Mueller-Dieckmann HJ, Kim KK, Yokota H, Kim R, Kim SH; , Proc Natl Acad Sci U S A 1998;95:15189-15193.: Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. PUBMED:9860944 EPMC:9860944

  3. Sousa MC, McKay DB; , Structure (Camb) 2001;9:1135-1141.: Structure of the universal stress protein of Haemophilus influenzae. PUBMED:11738040 EPMC:11738040

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006016

This entry represents a domain found in the universal stress protein UspA [ PUBMED:8152377 ], which is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA [ PUBMED:11738040 ] reveals an alpha/beta fold similar to that of the Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0577 protein, which binds ATP [ PUBMED:9860944 ], though UspA lacks ATP-binding activity.

Proteins containing this domain include the TeaD protein from Halomonas elongata. TeaD regulates the ectoine uptake by the transporter TeaABC. TeaD shows an ATP-dependent oligomerisation [ PUBMED:20113006 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan HUP (CL0039), which has the following description:

The HUP class contains the HIGH-signature proteins, UspA superfamily and the PP-ATPase superfamily [1]. The HIGH superfamily has the HIGH Nucleotidyl transferases and the class I tRNA synthetases both of which have the HIGH and the KMSKS motif [1],[2]. The PP-loop ATPase named after the ATP PyroPhosphatase domain, was initially identified as a conserved amino acid sequence motif in four distinct groups of enzymes that catalyse the hydrolysis of the alpha-beta phosphate bond of ATP, namely GMP synthetases, argininosuccinate synthetases, asparagine synthetases, and ATP sulfurylases [3]. The USPA superfamily contains USPA, ETFP and Photolyases [1]

The clan contains the following 32 members:

Arginosuc_synth Asn_synthase ATP-sulfurylase ATP_bind_3 BshC CDPS Citrate_ly_lig CTP_transf_like Diphthami_syn_2 DNA_photolyase DPRP ETF FAD_syn HIGH_NTase1 HIGH_NTase1_ass NAD_synthase Pantoate_ligase PAPS_reduct QueC QueH ThiI tRNA-synt_1 tRNA-synt_1_2 tRNA-synt_1b tRNA-synt_1c tRNA-synt_1d tRNA-synt_1e tRNA-synt_1f tRNA-synt_1g tRNA_Me_trans UDPG_MGDP_dh_C Usp


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: MRC-LMB Genome group
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Griffiths-Jones SR , Kerk D , Studholme DJ
Number in seed: 159
Number in full: 62462
Average length of the domain: 136.1 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 60.62 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 141
Family (HMM) version: 29
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Usp domain has been found. There are 111 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A077ZQ64 View 3D Structure Click here
A0A0D2F3E4 View 3D Structure Click here
A0A0D2GT43 View 3D Structure Click here
A0A0H3GLC0 View 3D Structure Click here
A0A0H3GNX7 View 3D Structure Click here
A0A0H3GPI2 View 3D Structure Click here
A0A0H3GQ74 View 3D Structure Click here
A0A0H3GVY1 View 3D Structure Click here
A0A0H3GWU9 View 3D Structure Click here
A0A0H3GX13 View 3D Structure Click here
A0A0N7KH89 View 3D Structure Click here
A0A0N7KI21 View 3D Structure Click here
A0A0P0VB72 View 3D Structure Click here
A0A0P0VMX2 View 3D Structure Click here
A0A0P0Y4W2 View 3D Structure Click here
A0A0P0Y881 View 3D Structure Click here
A0A0R0FC91 View 3D Structure Click here
A0A0R0G4A7 View 3D Structure Click here
A0A0R0JFL7 View 3D Structure Click here
A0A0R0K8D7 View 3D Structure Click here
A0A0R0L4D0 View 3D Structure Click here
A0A0R0L852 View 3D Structure Click here
A0A0R4J3L4 View 3D Structure Click here
A0A175VSN2 View 3D Structure Click here
A0A175VWF3 View 3D Structure Click here
A0A178VQ59 View 3D Structure Click here
A0A1C1C751 View 3D Structure Click here
A0A1C1CRM6 View 3D Structure Click here
A0A1D6G8D5 View 3D Structure Click here
A0A1D6GA16 View 3D Structure Click here
A0A1D6GHY9 View 3D Structure Click here
A0A1D6GPF6 View 3D Structure Click here
A0A1D6GPU8 View 3D Structure Click here
A0A1D6HL18 View 3D Structure Click here
A0A1D6I421 View 3D Structure Click here
A0A1D6IEQ6 View 3D Structure Click here
A0A1D6J571 View 3D Structure Click here
A0A1D6JZ20 View 3D Structure Click here
A0A1D6KWQ4 View 3D Structure Click here
A0A1D6L4K8 View 3D Structure Click here