Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
108  structures 7103  species 0  interactions 33379  sequences 219  architectures

Family: CSD (PF00313)

Summary: 'Cold-shock' DNA-binding domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Cold-shock domain". More...

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
SymbolCSD
PfamPF00313
Pfam clanCL0021
InterProIPR002059
PROSITEPDOC00304
SCOPe1mjc / SUPFAM
CDDcd04458

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

  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" (PDF). 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. doi:10.1007/bf00037080. 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

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

'Cold-shock' DNA-binding domain Provide feedback

No Pfam abstract.

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 (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.

Domain organisation

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

Loading domain graphics...

Alignments

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...

View options

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.

  Seed
(34)
Full
(33379)
Representative proteomes UniProt
(133987)
RP15
(3822)
RP35
(14238)
RP55
(33133)
RP75
(57129)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(34)
Full
(33379)
Representative proteomes UniProt
(133987)
RP15
(3822)
RP35
(14238)
RP55
(33133)
RP75
(57129)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(34)
Full
(33379)
Representative proteomes UniProt
(133987)
RP15
(3822)
RP35
(14238)
RP55
(33133)
RP75
(57129)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

HMM logo

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...

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.

Note: You can also download the data file for the tree.

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: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
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 View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -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: 24
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

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.

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.

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.

Protein Predicted structure External Information
A0A0G2KDN7 View 3D Structure Click here
A0A0P0WPY9 View 3D Structure Click here
A0A0R0EDH9 View 3D Structure Click here
A0A0R0HF66 View 3D Structure Click here
A0A0R4IRA3 View 3D Structure Click here
A0A2R8QTF0 View 3D Structure Click here
A0A2R8QTF0 View 3D Structure Click here
A0A2R8QTF0 View 3D Structure Click here
A0A2R8QTF0 View 3D Structure Click here
A0A2R8QTF0 View 3D Structure Click here
A2ZU70 View 3D Structure Click here
A4HW60 View 3D Structure Click here
A4I3F8 View 3D Structure Click here
A4I6Q9 View 3D Structure Click here
A4I6R0 View 3D Structure Click here
B5DE31 View 3D Structure Click here
B7Z0E2 View 3D Structure Click here
B7Z0E2 View 3D Structure Click here
B7Z0E2 View 3D Structure Click here
B7Z0E2 View 3D Structure Click here
B7Z0E2 View 3D Structure Click here
B9F7B8 View 3D Structure Click here
C0PLI2 View 3D Structure Click here
D3ZEV0 View 3D Structure Click here
D3ZIK1 View 3D Structure Click here
D3ZZA6 View 3D Structure Click here
D4A3P0 View 3D Structure Click here
E7F3W9 View 3D Structure Click here
F1R500 View 3D Structure Click here
G5EDV3 View 3D Structure Click here
I1JSF3 View 3D Structure Click here
I1JZ92 View 3D Structure Click here
I1KA68 View 3D Structure Click here
I1LPN7 View 3D Structure Click here
I6WZM9 View 3D Structure Click here
K7K6H1 View 3D Structure Click here
K7MH03 View 3D Structure Click here
O62213 View 3D Structure Click here
O65639 View 3D Structure Click here
O75534 View 3D Structure Click here
O75534 View 3D Structure Click here
O75534 View 3D Structure Click here
O75534 View 3D Structure Click here
O75534 View 3D Structure Click here
P0A968 View 3D Structure Click here
P0A972 View 3D Structure Click here
P0A976 View 3D Structure Click here
P0A978 View 3D Structure Click here
P0A982 View 3D Structure Click here
P0A986 View 3D Structure Click here
P0A9X9 View 3D Structure Click here
P0A9Y6 View 3D Structure Click here
P16989 View 3D Structure Click here
P18395 View 3D Structure Click here
P18395 View 3D Structure Click here
P18395 View 3D Structure Click here
P18395 View 3D Structure Click here
P18395 View 3D Structure Click here
P36995 View 3D Structure Click here
P62960 View 3D Structure Click here
P62961 View 3D Structure Click here
P67809 View 3D Structure Click here
P91306 View 3D Structure Click here
P91398 View 3D Structure Click here
P92186 View 3D Structure Click here
P9WP75 View 3D Structure Click here
Q2FUQ9 View 3D Structure Click here
Q2FYN2 View 3D Structure Click here
Q2G009 View 3D Structure Click here
Q38896 View 3D Structure Click here
Q41188 View 3D Structure Click here
Q45KJ6 View 3D Structure Click here
Q4CKN9 View 3D Structure Click here
Q4CN63 View 3D Structure Click here
Q4DA79 View 3D Structure Click here
Q4DCA9 View 3D Structure Click here
Q4DL89 View 3D Structure Click here
Q4DSM4 View 3D Structure Click here
Q62764 View 3D Structure Click here
Q63430 View 3D Structure Click here
Q6PHF1 View 3D Structure Click here
Q6YUR8 View 3D Structure Click here
Q6ZN17 View 3D Structure Click here
Q803L0 View 3D Structure Click here
Q84UR8 View 3D Structure Click here
Q8I248 View 3D Structure Click here
Q8K3Y3 View 3D Structure Click here
Q91W50 View 3D Structure Click here
Q91W50 View 3D Structure Click here
Q91W50 View 3D Structure Click here
Q91W50 View 3D Structure Click here
Q91W50 View 3D Structure Click here
Q91YQ3 View 3D Structure Click here
Q94C69 View 3D Structure Click here
Q95RE4 View 3D Structure Click here
Q9CR86 View 3D Structure Click here
Q9H9Z2 View 3D Structure Click here
Q9JKB3 View 3D Structure Click here
Q9VRN5 View 3D Structure Click here
Q9VVA0 View 3D Structure Click here
Q9WU49 View 3D Structure Click here
Q9Y2T7 View 3D Structure Click here
Q9Y2V2 View 3D Structure Click here
Q9Y534 View 3D Structure Click here
Q9Z2C8 View 3D Structure Click here