Summary: 'Cold-shock' DNA-binding domain
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Cold-shock domain Edit Wikipedia article
| CSD | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 solution structure of the single-stranded dna-binding cold shock domain (csd) of human y-box protein 1 (yb1) determined by nmr (10 lowest energy structures) | |||||||||
| Identifiers | |||||||||
| Symbol | CSD | ||||||||
| Pfam | PF00313 | ||||||||
| Pfam clan | CL0021 | ||||||||
| InterPro | IPR002059 | ||||||||
| PROSITE | PDOC00304 | ||||||||
| SCOPe | 1mjc / SUPFAM | ||||||||
| CDD | cd04458 | ||||||||
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In molecular biology, the cold-shock domain (CSD) is a protein domain of about 70 amino acids which has been found in prokaryotic and eukaryotic DNA-binding proteins.[1][2][3] Part of this domain is highly similar to the RNP-1 RNA-binding motif.[4]
When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees Celsius, a 4–5 hour lag phase occurs, after which growth is resumed at a reduced rate.[5] During the lag phase, the expression of around 13 proteins, which contain cold shock domains is increased 2–10 fold.[6] These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid.[5]
References
- ^ Doniger J, Landsman D, Gonda MA, Wistow G (April 1992). "The product of unr, the highly conserved gene upstream of N-ras, contains multiple repeats similar to the cold-shock domain (CSD), a putative DNA-binding motif". New Biol. 4 (4): 389–95. PMID 1622933.
- ^ Wistow G (April 1990). "Cold shock and DNA binding" (PDF). Nature. 344 (6269): 823–4. doi:10.1038/344823c0. PMID 2184368.
- ^ Jones PG, Inouye M (March 1994). "The cold-shock response--a hot topic". Mol. Microbiol. 11 (5): 811–8. doi:10.1111/j.1365-2958.1994.tb00359.x. PMID 8022259.
- ^ Landsman D (June 1992). "RNP-1, an RNA-binding motif is conserved in the DNA-binding cold shock domain". Nucleic Acids Res. 20 (11): 2861–4. doi:10.1093/nar/20.11.2861. PMC 336933. PMID 1614871.
- ^ a b Obokata J, Ohme M, Hayashida N (October 1991). "Nucleotide sequence of a cDNA clone encoding a putative glycine-rich protein of 19.7 kDa in Nicotiana sylvestris". Plant Mol. Biol. 17 (4): 953–5. doi:10.1007/bf00037080. PMID 1912512.
- ^ Tafuri SR, Wolffe AP (November 1990). "Xenopus Y-box transcription factors: molecular cloning, functional analysis and developmental regulation". Proc. Natl. Acad. Sci. U.S.A. 87 (22): 9028–32. doi:10.1073/pnas.87.22.9028. PMC 55094. PMID 2247479.
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No Pfam abstract.
Literature references
-
Schindelin H, Jiang W, Inouye M, Heinemann U; , Proc Natl Acad Sci U S A 1994;91:5119-5123.: Crystal structure of CspA, the major cold shock protein of Escherichia coli. PUBMED:8197194 EPMC:8197194
Internal database links
| SCOOP: | OB_RNB Rho_RNA_bind S1 |
| Similarity to PfamA using HHSearch: | Rho_RNA_bind OB_RNB |
External database links
| HOMSTRAD: | csp |
| PRINTS: | PR00050 |
| PROSITE: | PDOC00304 |
| SCOP: | 1mjc |
This tab holds annotation information from the InterPro database.
InterPro entry IPR002059
When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate [ PUBMED:1912512 ]. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [ PUBMED:2247479 ], is increased 2-10 fold. These so-called 'cold shock' proteins (CSPs) are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid [ PUBMED:1912512 ]. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [ PUBMED:1622933 , PUBMED:2184368 , PUBMED:8022259 ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [ PUBMED:1614871 ] to the RNP-1 RNA-binding motif.
CSPs include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSPs are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA [ PUBMED:8321288 ]. CSPs are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD [ PUBMED:11851341 ], regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Molecular function | nucleic acid binding (GO:0003676) |
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 OB (CL0021), which has the following description:
The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin [1]. The common part of the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands [1].
The clan contains the following 112 members:
BOF BRCA-2_OB1 BRCA-2_OB3 CcmE CDC13_N Cdc13_OB2 CDC24_OB1 CDC24_OB2 CDC24_OB3 CSD CSD2 CusF_Ec CysA_C_terminal DNA_ligase_A_C DNA_ligase_C DNA_ligase_OB DNA_ligase_OB_2 DNA_pol_D_N DUF1344 DUF1449 DUF2110 DUF223 DUF2815 DUF3127 DUF3217 DUF3299 DUF5666 DUF6484 DUF961 EFP eIF-1a eIF-5a Elong-fact-P_C EutN_CcmL EXOSC1 FbpC_C_terminal Fimbrial_PilY2 GlcV_C_terminal Gp138_N gp32 Gp5_OB HIN HROB ID MCM_OB mRNA_cap_C MRP-S35 NfeD NigD_N NlpE_C OB_aCoA_assoc OB_Dis3 OB_MalK OB_NTP_bind OB_RNB PCB_OB Phage_base_V Phage_DNA_bind Phage_SSB Pol_alpha_B_N POT1 POT1PC Prot_ATP_ID_OB Prot_ATP_OB_N RecG_wedge RecJ_OB RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 Rep_fac-A_C REPA_OB_2 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 Ribosomal_S28e Ribosomal_S4e RMI1_C RMI1_N RMI2 RNA_pol_Rbc25 RNA_pol_Rpb8 RNA_pol_RpbG RNase_II_C_S1 RPA43_OB Rrp44_CSD1 Rrp44_S1 RsgA_N RuvA_N S1 S1-like S1_2 SfsA_N SSB ssDBP Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TPP1 TRAM TRAM_2 tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind TTC5_OB WCOBAlignments
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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| Seed (34) |
Full (33379) |
Representative proteomes | UniProt (133987) |
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| RP15 (3822) |
RP35 (14238) |
RP55 (33133) |
RP75 (57129) |
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| HTML | |||||||
| PP/heatmap | 1 | ||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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| Seed (34) |
Full (33379) |
Representative proteomes | UniProt (133987) |
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|---|---|---|---|---|---|---|---|
| RP15 (3822) |
RP35 (14238) |
RP55 (33133) |
RP75 (57129) |
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| Raw Stockholm | |||||||
| Gzipped | |||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
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Trees
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
| Seed source: | Prosite |
| Previous IDs: | none |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Finn RD 
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| Number in seed: | 34 |
| Number in full: | 33379 |
| Average length of the domain: | 65.20 aa |
| Average identity of full alignment: | 39 % |
| Average coverage of the sequence by the domain: | 54.45 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 66 | ||||||||||||
| Family (HMM) version: | 24 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Structures
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 CSD domain has been found. There are 108 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.
