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 clan

1mjc / SUPFAM

Available protein structures:
Pfam	structures / ECOD
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

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 4â€“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 2â€“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): 389â€“95. PMID 1622933.
^ Wistow G (April 1990). "Cold shock and DNA binding" (PDF). Nature. 344 (6269): 823â€“4. doi:10.1038/344823c0. PMID 2184368.
^ Jones PG, Inouye M (March 1994). "The cold-shock response--a hot topic". Mol. Microbiol. 11 (5): 811â€“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): 2861â€“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): 953â€“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): 9028â€“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

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 WCOB

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...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
UniProt: alignment generated by searching the UniProtKB sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
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PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.

Reformatting

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Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

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)
	Seed (34)	Full (33379)	RP15 (3822)	RP35 (14238)	RP55 (33133)	RP75 (57129)	UniProt (133987)
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, not generated, — not available.

Format an alignment

	Seed (34)	Full (33379)	Representative proteomes				UniProt (133987)
	Seed (34)	Full (33379)	RP15 (3822)	RP35 (14238)	RP55 (33133)	RP75 (57129)	UniProt (133987)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	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)
	Seed (34)	Full (33379)	RP15 (3822)	RP35 (14238)	RP55 (33133)	RP75 (57129)	UniProt (133987)
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

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

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

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Colour assignments

Archea	Eukaryota
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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...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

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class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

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".

Sub-species

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.

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

Species trees

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.

Interactive tree

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:

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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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Family: CSD (PF00313)

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