Summary: Elongation factor G, domain IV
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|Alt. names||Elongation factor G, EF-G|
|PDB structures||RCSB PDB PDBe PDBsum|
|Translation elongation factor EFG/EF2|
|SCOP2||1n0u / SCOPe / SUPFAM|
|EFG/EF2, domain IV|
EF-G (elongation factor G, historically known as translocase) is a prokaryotic elongation factor involved in protein translation. As a GTPase, EF-G catalyzes the movement (translocation) of transfer RNA (tRNA) and messenger RNA (mRNA) through the ribosome.
Encoded by the fusA gene on the str operon, EF-G is made up of 704 amino acids that form 5 domains, labeled Domain I through Domain V. Domain I may be referred to as the G-domain or as Domain I(G), since it binds to and hydrolyzes guanosine triphosphate (GTP). Domain I also helps EF-G bind to the ribosome, and contains the N-terminal of the polypeptide chain. Domain IV is important for translocation, as it undergoes a significant conformational change and enters the A site on the 30S ribosomal subunit, pushing the mRNA and tRNA molecules from the A site to the P site.
The five domains may be also separated into two super-domains. Super-domain I consists of Domains I and II, and super-domain II consists of Domains III - IV. Throughout translocation, super-domain I will remain relatively unchanged, as it is responsible for binding tightly to the ribosome. However, super-domain II will undergo a large rotational motion from the pre-translocational (PRE) state to the post-translocational (POST) state. Super-domain I is similar to the corresponding sections of EF-Tu. Super-domain II in the POST state mimics the tRNA molecule of the EF-Tu â€¢ GTP â€¢ aa-tRNA ternary complex.
EF-G on the ribosome
Binding to L7/L12
L7/L12 is only a multicopy protein on the large ribosomal subunit of the bacterial ribosome that binds to certain GTPases, like Initiation Factor 2, Elongation factor-Tu, Release Factor 3, and EF-G. Specifically, the C-terminal of L7/L12 will bind to EF-G and is necessary for GTP hydrolysis.
Interaction with the GTPase Associated Center
The GTPase Associated Center (GAC) is a region on the large ribosomal subunit that consists of two smaller regions of 23S ribosomal RNA called the L11 stalk and the sarcin-ricin loop (SRL). As a highly conserved rRNA loop in evolution, the SRL is critical in helping GTPases bind to the ribosome, but is not essential for GTP hydrolysis. There is some evidence to support that a phosphate oxygen in the A2662 residue of the SRL may help hydrolyze GTP.
Function in protein elongation
EF-G catalyzes the translocation of the tRNA and mRNA down the ribosome at the end of each round of polypeptide elongation. In this process, the peptidyl transferase center (PTC) has catalyzed the formation of a peptide bond between amino acids, moving the polypeptide chain from the P site tRNA to the A site tRNA. The 50S and 30S ribosomal subunits are now allowed to rotate relative to each other by approximately 7Â°. The subunit rotation is coupled with the movement of the 3' ends of both tRNA molecules on the large subunit from the A and P sites to the P and E sites, respectively, while the anticodon loops remain unshifted. This rotated ribosomal intermediate, in which the first tRNA occupies a hybrid A/P position and the second tRNA occupies a hybrid P/E position is a substrate for EF-G-GTP.
As a GTPase, EF-G binds to the rotated ribosome near the A site in its GTP-bound state, and hydrolyzes GTP, releasing GDP and inorganic phosphate:
The hydrolysis of GTP allows for a large conformational change within EF-G, forcing the A/P tRNA to fully occupy the P site, the P/E tRNA to fully occupy the E site (and exit the ribosome complex), and the mRNA to shift three nucleotides down relative to the ribosome. The GDP-bound EF-G molecule then dissociates from the complex, leaving another free A-site where the elongation cycle can start again.
Function in protein termination
Protein elongation continues until a stop codon appears on the mRNA. A Class I release factor (RF1 or RF2) binds to the stop codon, which induces hydrolysis of the tRNA-peptide bond in the P site, allowing the newly-formed protein to exit the ribosome. The nascent peptide continues to fold and leaves the 70S ribosome, the mRNA, the deacylated tRNA (P site), and the Class I release factor (A site).
In a GTP-dependent manner, the subsequent recycling is catalyzed by a Class II release factor named RF3/prfC, Ribosome recycling factor (RRF), Initiation Factor 3 (IF3) and EF-G. The protein RF3 releases the Class I release factor so that it may occupy the ribosomal A site. EF-G hydrolyzes GTP and undergoes a large conformational change to push RF3 down the ribosome, which occurs alongside tRNA dissociation and promotes the ribosomal subunit rotation. This motion actively splits the B2a/B2b bridge, which connects the 30S and the 50S subunits, so that the ribosome can split. IF3 then isolates the 30S subunit to prevent re-association of the large and small subunits.
For example, the antibiotic thiostrepton prevents EF-G from binding stably to the ribosome, while the antibiotics dityromycin and GE82832 inhibit the activity of EF-G by preventing the translocation of the A site tRNA. Dityromycin and GE82832 do not affect the binding of EF-G to the ribosome, however.
The antibiotic fusidic acid is known to inhibit Staphylococcus aureus and other bacteria by binding to EF-G after one translocation event on the ribosome, preventing EF-G from dissociating. However, some bacterial strains have developed resistance to fusidic acid due to point mutations in the fusA gene, which prevents fusidic acid from binding to EF-G.
EF-G has a complex evolutionary history, with numerous paralogous versions of the factor present in bacteria, suggesting subfunctionalization of different EF-G variants.
Elongation factors exist in all three domains of life with similar function on the ribosome. The eukaryotic and archeal homologs of EF-G are eEF2 and aEF2, respectively. In bacteria (and some archaea), the fusA gene that encodes EF-G is found within the conserved str gene with the sequence 5â€² - rpsL - rpsG - fusA - tufA - 3â€². However, two other major forms of EF-G exist in some species of Spirochetes, Planctomycetes, and Î´-Proteobacteria, which form the spd group of bacteria that have elongation factors spdEFG1 and spdEFG2.
From spdEFG1 and spdEFG2 evolved the mitochondrial elongation factors mtEFG1 (GFM1) and mtEFG2 (GFM2), respectively. The two roles of EF-G in elongation and termination of protein translation are split amongst the mitochondrial elongation factors, with mtEFG1 responsible for translocation and mtEFG2 responsible for termination and ribosomal recycling with mitochondrial RRF.
- Prokaryotic elongation factors
- EF-Ts (elongation factor thermo stable)
- EF-Tu (elongation factor thermo unstable)
- EF-P (elongation factor P)
- eEF2 (eukaryotic elongation factor 2)
- Protein translation
- Shoji, S; Walker, SE; Fredrick, K (2009). "Ribosomal translocation: one step closer to the molecular mechanism". ACS Chem Biol. 4 (2): 93â€“107. doi:10.1021/cb8002946. PMCÂ 3010847. PMIDÂ 19173642.
- Post, L. E.; Nomura, M. (1980-05-25). "DNA sequences from the str operon of Escherichia coli". The Journal of Biological Chemistry. 255 (10): 4660â€“4666. doi:10.1016/S0021-9258(19)85545-X. ISSNÂ 0021-9258. PMIDÂ 6989816.
- Liu, Kaixian; Rehfus, Joseph E.; Mattson, Elliot; Kaiser, Christian M. (2017-07-01). "The ribosome destabilizes native and non-native structures in a nascent multidomain protein". Protein Science. 26 (7): 1439â€“1451. doi:10.1002/pro.3189. ISSNÂ 1469-896X. PMCÂ 5477528. PMIDÂ 28474852.
- Carlson, Markus A.; Haddad, Bassam G.; Weis, Amanda J.; Blackwood, Colby S.; Shelton, Catherine D.; Wuerth, Michelle E.; Walter, Justin D.; Spiegel, Paul Clint (2017-06-01). "Ribosomal protein L7/L12 is required for GTPase translation factors EF-G, RF3, and IF2 to bind in their GTP state to 70S ribosomes". The FEBS Journal. 284 (11): 1631â€“1643. doi:10.1111/febs.14067. ISSNÂ 1742-4658. PMCÂ 5568246. PMIDÂ 28342293.
- Salsi, Enea; Farah, Elie; Dann, Jillian; Ermolenko, Dmitri N. (2014). "Following movement of domain IV of elongation factor G during ribosomal translocation". Proceedings of the National Academy of Sciences. 111 (42): 15060â€“15065. Bibcode:2014PNAS..11115060S. doi:10.1073/pnas.1410873111. PMCÂ 4210333. PMIDÂ 25288752.
- Lin, Jinzhong; Gagnon, Matthieu G.; Bulkley, David; Steitz, Thomas A. (2015). "Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation". Cell. 160 (1â€“2): 219â€“227. doi:10.1016/j.cell.2014.11.049. PMCÂ 4297320. PMIDÂ 25594181.
- Li, Wen; Trabuco, Leonardo G.; Schulten, Klaus; Frank, Joachim (2011-05-01). "Molecular dynamics of EF-G during translocation". Proteins: Structure, Function, and Bioinformatics. 79 (5): 1478â€“1486. doi:10.1002/prot.22976. ISSNÂ 1097-0134. PMCÂ 3132869. PMIDÂ 21365677.
- Zhang, Dejiu; Yan, Kaige; Zhang, Yiwei; Liu, Guangqiao; Cao, Xintao; Song, Guangtao; Xie, Qiang; Gao, Ning; Qin, Yan (2015). "New insights into the enzymatic role of EF-G in ribosome recycling". Nucleic Acids Research. 43 (21): 10525â€“33. doi:10.1093/nar/gkv995. PMCÂ 4666400. PMIDÂ 26432831.
- Nyborg, J.; Nissen, P.; Kjeldgaard, M.; Thirup, S.; Polekhina, G.; Clark, B. F. (March 1996). "Structure of the ternary complex of EF-Tu: macromolecular mimicry in translation". Trends in Biochemical Sciences. 21 (3): 81â€“82. doi:10.1016/S0968-0004(96)30008-X. ISSNÂ 0968-0004. PMIDÂ 8882578.
- Mandava, C. S.; Peisker, K.; Ederth, J.; Kumar, R.; Ge, X.; Szaflarski, W.; Sanyal, S. (2011-11-18). "Bacterial ribosome requires multiple L12 dimers for efficient initiation and elongation of protein synthesis involving IF2 and EF-G". Nucleic Acids Research. 40 (5): 2054â€“2064. doi:10.1093/nar/gkr1031. ISSNÂ 0305-1048. PMCÂ 3299993. PMIDÂ 22102582.
- Maklan, E. J. (2012). Genetic and Biochemical Analysis of the GTPase Associated Center of the Ribosome. UC Santa Cruz. Merritt ID: ark:/13030/m5js9t4d. Retrieved from https://escholarship.org/uc/item/7gh9v43h
- Shi, Xinying; Khade, Prashant K.; Sanbonmatsu, Karissa Y.; Joseph, Simpson (2012). "Functional Role of the Sarcinâ€“Ricin Loop of the 23S rRNA in the Elongation Cycle of Protein Synthesis". Journal of Molecular Biology. 419 (3â€“4): 125â€“138. doi:10.1016/j.jmb.2012.03.016. PMCÂ 3348345. PMIDÂ 22459262.
- Choi, Junhong; Puglisi, Joseph D. (2017). "Three tRNAs on the ribosome slow translation elongation". Proceedings of the National Academy of Sciences. 114 (52): 13691â€“13696. doi:10.1073/pnas.1719592115. PMCÂ 5748233. PMIDÂ 29229848.
- Guo, Z.; Noller, H. F. (2012). "Rotation of the head of the 30S ribosomal subunit during mRNA translocation". Proceedings of the National Academy of Sciences. 109 (50): 20391â€“20394. Bibcode:2012PNAS..10920391G. doi:10.1073/pnas.1218999109. PMCÂ 3528506. PMIDÂ 23188795.
- da Cunha, CE; Belardinelli, R; Peske, F; Holtkamp, W; Wintermeyer, W; Rodnina, MV (2013). "Dual use of GTP hydrolysis by elongation factor G on the ribosome". Translation. 1 (1): e24315. doi:10.4161/trla.24315. PMCÂ 4718068. PMIDÂ 26824016.
- Das, Debasis; Samanta, Dibyendu; Bhattacharya, Arpita; Basu, Arunima; Das, Anindita; Ghosh, Jaydip; Chakrabarti, Abhijit; Gupta, Chanchal Das (2017-01-18). "A Possible Role of the Full-Length Nascent Protein in Post-Translational Ribosome Recycling". PLOS ONE. 12 (1): e0170333. Bibcode:2017PLoSO..1270333D. doi:10.1371/journal.pone.0170333. ISSNÂ 1932-6203. PMCÂ 5242463. PMIDÂ 28099529.
- Zavialov AV, Hauryliuk VV, Ehrenberg M (2005). "Splitting of the posttermination ribosome into subunits by the concerted action of RRF and EF-G". Molecular Cell. 18 (6): 675â€“686. doi:10.1016/j.molcel.2005.05.016. PMIDÂ 15949442.
- Hirokawa, Go; Nijman, Romana M.; Raj, V. Samuel; Kaji, Hideko; Igarashi, Kazuei; Kaji, Akira (2005-08-01). "The role of ribosome recycling factor in dissociation of 70S ribosomes into subunits". RNA. 11 (8): 1317â€“1328. doi:10.1261/rna.2520405. ISSNÂ 1355-8382. PMCÂ 1370814. PMIDÂ 16043510.
- Walter, Justin D.; Hunter, Margaret; Cobb, Melanie; Traeger, Geoff; Spiegel, P. Clint (2012-01-01). "Thiostrepton inhibits stable 70S ribosome binding and ribosome-dependent GTPase activation of elongation factor G and elongation factor 4". Nucleic Acids Research. 40 (1): 360â€“370. doi:10.1093/nar/gkr623. ISSNÂ 0305-1048. PMCÂ 3245911. PMIDÂ 21908407.
- Bulkley, David; Brandi, Letizia; Polikanov, Yury S.; Fabbretti, Attilio; Oâ€™Connor, Michael; Gualerzi, Claudio O.; Steitz, Thomas A. (2014). "The Antibiotics Dityromycin and GE82832 Bind Protein S12 and Block EF-G-Catalyzed Translocation". Cell Reports. 6 (2): 357â€“365. doi:10.1016/j.celrep.2013.12.024. PMCÂ 5331365. PMIDÂ 24412368.
- Belardinelli, Riccardo; Rodnina, Marina V. (2017-09-05). "Effect of Fusidic Acid on the Kinetics of Molecular Motions During EF-G-Induced Translocation on the Ribosome". Scientific Reports. 7 (1): 10536. Bibcode:2017NatSR...710536B. doi:10.1038/s41598-017-10916-8. ISSNÂ 2045-2322. PMCÂ 5585275. PMIDÂ 28874811.
- Koripella, Ravi Kiran; Chen, Yang; Peisker, Kristin; Koh, Cha San; Selmer, Maria; Sanyal, Suparna (2012). "Mechanism of Elongation Factor-G-mediated Fusidic Acid Resistance and Fitness Compensation inStaphylococcus aureus". Journal of Biological Chemistry. 287 (36): 30257â€“30267. doi:10.1074/jbc.m112.378521. PMCÂ 3436278. PMIDÂ 22767604.
- Macvanin M, Hughes D (June 2005). "Hyper-susceptibility of a fusidic acid-resistant mutant of Salmonella to different classes of antibiotics". FEMS Microbiology Letters. 247 (2): 215â€“20. doi:10.1016/j.femsle.2005.05.007. PMIDÂ 15935566.
- Macvanin M, Johanson U, Ehrenberg M, Hughes D (July 2000). "Fusidic acid-resistant EF-G perturbs the accumulation of ppGpp". Molecular Microbiology. 37 (1): 98â€“107. doi:10.1046/j.1365-2958.2000.01967.x. PMIDÂ 10931308. S2CIDÂ 10307058.
- G C Atkinson; S L Baldauf (2011). "Evolution of elongation factor G and the origins of mitochondrial and chloroplast forms". Molecular Biology and Evolution. 28 (3): 1281â€“92. doi:10.1093/molbev/msq316. PMIDÂ 21097998.
- Margus, TÃµnu; Remm, Maido; Tenson, Tanel (2011-08-04). "A Computational Study of Elongation Factor G (EFG) Duplicated Genes: Diverged Nature Underlying the Innovation on the Same Structural Template". PLOS ONE. 6 (8): e22789. Bibcode:2011PLoSO...622789M. doi:10.1371/journal.pone.0022789. ISSNÂ 1932-6203. PMCÂ 3150367. PMIDÂ 21829651.
- Carbone, Christine E.; Loveland, Anna B.; Gamper, Howard B.; Hou, Ya-Ming; Demo, Gabriel; Korostelev, Andrei A. (December 2021). "Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP". Nature Communications. 12 (1): 7236. doi:10.1038/s41467-021-27415-0.
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.
Elongation factor G, domain IV Provide feedback
This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold.
Internal database links
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR005517
Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [ PUBMED:12762045 , PUBMED:15922593 , PUBMED:12932732 ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution.
Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [ PUBMED:12762009 , PUBMED:12762047 ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome.
EF2 has five domains. This entry represents domain IV found in EF2 (or EF-G) of both prokaryotes and eukaryotes. The EF2-GTP-ribosome complex undergoes extensive structural rearrangement for tRNA-mRNA movement to occur. Domain IV, which extends from the 'body' of the EF2 molecule much like a lever arm, facilitates the movement of peptidyl-tRNA from the A to the P site, being critical for the structural transition to take place [ PUBMED:25288752 ].
Included in this entry is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins that is homologous to domain IV of EF-G. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA [ PUBMED:11735030 , PUBMED:1935960 , PUBMED:15922593 , PUBMED:1602493 , PUBMED:8159735 , PUBMED:10837219 , PUBMED:12471894 , PUBMED:16213500 , PUBMED:12932345 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||GTP binding (GO:0005525)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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This example describes an architecture with one
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EGFdomains, and finally a single
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This superfamily contains a wide range of families that possess a structure similar to the second domain of ribosomal S5 protein.
The clan contains the following 18 members:ChlI DNA_gyraseB DNA_mis_repair EFG_IV Fae GalKase_gal_bdg GHMP_kinases_N IGPD Lon_C LpxC Morc6_S5 Ribonuclease_P Ribosomal_S5_C Ribosomal_S9 RNase_PH Topo-VIb_trans UPF0029 Xol-1_N
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Seed source:||Pfam-B_40 (release 2.1)|
|Author:||Bateman A , Griffiths-Jones SR|
|Number in seed:||64|
|Number in full:||21771|
|Average length of the domain:||118.70 aa|
|Average identity of full alignment:||32 %|
|Average coverage of the sequence by the domain:||16.22 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||21|
|Download:||download the raw HMM for this family|
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
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 EFG_IV domain has been found. There are 208 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.
Loading structure mapping...
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.