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61  structures 3908  species 1  interaction 14886  sequences 69  architectures

Family: CSD (PF00313)

Summary: 'Cold-shock' DNA-binding domain

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Cold-shock domain Edit Wikipedia article

CSD
PDB 1h95 EBI.jpg
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
SCOP 1mjc
SUPERFAMILY 1mjc

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[edit]

  1. ^ 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. 
  2. ^ Wistow G (April 1990). "Cold shock and DNA binding". Nature 344 (6269): 823–4. doi:10.1038/344823c0. PMID 2184368. 
  3. ^ 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. 
  4. ^ 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. 
  5. ^ 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. PMID 1912512. 
  6. ^ 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. 

This article incorporates text from the public domain Pfam and InterPro IPR002059

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Literature references

  1. 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

External database links

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 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.

Gene Ontology

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Domain organisation

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Alignments

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(40)
Full
(14886)
Representative proteomes NCBI
(7958)
Meta
(3141)
RP15
(1082)
RP35
(2120)
RP55
(2935)
RP75
(3740)
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Format an alignment

  Seed
(40)
Full
(14886)
Representative proteomes NCBI
(7958)
Meta
(3141)
RP15
(1082)
RP35
(2120)
RP55
(2935)
RP75
(3740)
Alignment:
Format:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(40)
Full
(14886)
Representative proteomes NCBI
(7958)
Meta
(3141)
RP15
(1082)
RP35
(2120)
RP55
(2935)
RP75
(3740)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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Curation and family details

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Seed source: Prosite
Previous IDs: none
Type: Domain
Author: Finn RD
Number in seed: 40
Number in full: 14886
Average length of the domain: 65.20 aa
Average identity of full alignment: 46 %
Average coverage of the sequence by the domain: 67.33 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.7
Model length: 66
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Interactions

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CSD

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 61 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 seqence.

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