The domain within your query sequence starts at position 65 and ends at position 130; the E-value for the CSP domain shown below is 3.91e-22.

KGVCKCFCRSKGHGFITPGDGGPDIFLHISDVEGEYVPVEGDEVTYKMCSIPPKNEKLQA
VEVVIT

CSP

Cold shock protein domain

• SMART accession number: SM00357
• Description: RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
• Interpro abstract (IPR011129):

  A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic single-strand nucleic-acid binding proteins [ (PUBMED:1622933) (PUBMED:2184368) (PUBMED:8022259) (PUBMED:9586995) (PUBMED:10446180) ]. This domain, which is known as the 'cold-shock domain' (CSD) is present in the proteins listed below.

  • Escherichia coli protein CS7.4 (gene cspA) which is induced in response to low temperature (cold-shock protein) and which binds to and stimulates the transcription of the CCAAT-containing promoters of the HN-S protein and of gyrA.
  • Transcription termination factor Rho, a prokaryotic protein which facilitates transcription termination.
  • Mammalian Y box binding protein 1 (YB1). A protein that binds to the CCAAT-containing Y box of mammalian HLA class II genes.
  • Xenopus Y box binding proteins -1 and -2 (Y1 and Y2). Proteins that bind to the CCAAT-containing Y box of Xenopus hsp70 genes.
  • Xenopus B box binding protein (YB3). YB3 binds the B box promoter element of genes transcribed by RNA polymerase III.
  • Enhancer factor I subunit A (EFI-A) (dbpB). A protein that also bind to CCAAT-motif in various gene promoters.
  • DbpA, a human DNA-binding protein of unknown specificity.
  • Bacillus subtilis cold-shock proteins cspB and cspC.
  • Streptomyces clavuligerus protein SC 7.0.
  • E. coli proteins cspB, cspC, cspD, cspE and cspF.
  • Unr, a mammalian gene encoded upstream of the N-ras gene. Unr contains nine repeats that are similar to the CSD domain. The function of Unr is not yet known but it could be a multivalent DNA-binding protein.
  • PPPin, a mammalian brain-specific protein that binds to histone mRNA and which is thought to play a role in the regulation of brain development.
• GO function: nucleic acid binding (GO:0003676)

There are 80336 CSP domains in 70472 proteins in SMART's nrdb database.

Cellular role (predicted cellular role)

Binding / catalysis: RNA-binding

Literature (relevant references for this domain)

Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

• Bogden CE, Fass D, Bergman N, Nichols MD, Berger JM
• The structural basis for terminator recognition by the Rho transcription termination factor.
• Mol Cell. 1999; 3: 487-93

The E. coli Rho protein disengages newly transcribed RNA from its DNA template, helping terminate certain transcripts. We have determined the X-ray crystal structure of the RNA-binding domain of Rho complexed to an RNA ligand. Filters that screen both ligand size and chemical functionality line the primary nucleic acid-binding site, imparting sequence specificity to a generic single-stranded nucleic acid-binding fold and explaining the preference of Rho for cytosine-rich RNA. The crystal packing reveals two Rho domain protomers bound to a single RNA with a single base spacer, suggesting that the strong RNA-binding sites of Rho may arise from pairing of RNA-binding modules. Dimerization of symmetric subunits on an asymmetric ligand is developed as a model for allosteric control in the action of the intact Rho hexamer.

• Allison TJ, Wood TC, Briercheck DM, Rastinejad F, Richardson JP, Rule GS
• Crystal structure of the RNA-binding domain from transcription termination factor rho.
• Nat Struct Biol. 1998; 5: 352-6

Transcription termination factor rho is an ATP-dependent hexameric helicase found in most eubacterial species. The Escherichia coli rho monomer consists of two domains, an RNA-binding domain (residues 1-130) and an ATPase domain (residues 131-419). The ATPase domain is homologous to the beta subunit of F1-ATPase. Here, we report that the crystal structure of the RNA-binding domain of rho (rho130) at 1.55 A confirms that rho130 contains the oligosaccharide/oligonucleotide-binding (OB) fold, a five stranded beta-barrel. The beta-barrel of rho130 is also surprisingly similar to the N-terminal beta-barrel of F1 ATPase, extending the applicability of F1 ATPase as a structural model for hexameric rho.

• Briercheck DM, Wood TC, Allison TJ, Richardson JP, Rule GS
• The NMR structure of the RNA binding domain of E. coli rho factor suggests possible RNA-protein interactions.
• Nat Struct Biol. 1998; 5: 393-9

Rho protein is an essential hexameric RNA-DNA helicase that binds nascent mRNA transcripts and terminates transcription in a wide variety of eubacterial species. The NMR solution structure of the RNA binding domain of rho, rho130, is presented. This structure consists of two sub-domains, an N-terminal three-helix bundle and a C-terminal beta-barrel that is structurally similar to the oligosaccharide/oligonucleotide binding (OB) fold. Chemical shift changes of rho130 upon RNA binding and previous mutagenetic analyses of intact rho suggest that residues Asp 60, Phe 62, Phe 64, and Arg 66 are critical for binding and support the hypothesis that ssRNA/ssDNA binding is localized in the beta-barrel sub-domain. On the basis of these studies and the tertiary structure of rho130, we propose that residues Asp 60, Phe 62, Phe 64, Arg 66, Tyr 80, Lys 105, and Arg 109 participate in RNA-protein interactions.

• Graumann PL, Marahiel MA
• A superfamily of proteins that contain the cold-shock domain.
• Trends Biochem Sci. 1998; 23: 286-90

Members of a family of cold-shock proteins (CSPs) are found throughout the eubacterial domain and appear to function as RNA-chaperones. They have been implicated in various cellular processes, including adaptation to low temperatures, cellular growth, nutrient stress and stationary phase. The discovery of a domain--the cold-shock domain--that shows strikingly high homology and similar RNA-binding properties to CSPs in a growing number of eukaryotic nucleic-acid-binding proteins suggests that these proteins have an ancient origin.

• Markus MA, Gerstner RB, Draper DE, Torchia DA
• The solution structure of ribosomal protein S4 delta41 reveals two subdomains and a positively charged surface that may interact with RNA.
• EMBO J. 1998; 17: 4559-71

S4 is one of the first proteins to bind to 16S RNA during assembly of the prokaryotic ribosome. Residues 43-200 of S4 from Bacillus stearothermophilus (S4 Delta41) bind specifically to both 16S rRNA and to a pseudoknot within the alpha operon mRNA. As a first step toward understanding how S4 recognizes and organizes RNA, we have solved the structure of S4 Delta41 in solution by multidimensional heteronuclear nuclear magnetic resonance spectroscopy. The fold consists of two globular subdomains, one comprised of four helices and the other comprised of a five-stranded antiparallel beta-sheet and three helices. Although cross-linking studies suggest that residues between helices alpha2 and alpha3 are close to RNA, the concentration of positive charge along the crevice between the two subdomains suggests that this could be an RNA-binding site. In contrast to the L11 RNA-binding domain studied previously, S4 Delta41 shows no fast local motions, suggesting that it has less capacity for refolding to fit RNA. The independently determined crystal structure of S4 Delta41 shows similar features, although there is small rotation of the subdomains compared with the solution structure. The relative orientation of the subdomains in solution will be verified with further study.

• Schindelin H, Marahiel MA, Heinemann U
• Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein.
• Nature. 1993; 364: 164-8

The cold-shock response in both Escherichia coli and Bacillus subtilis is induced by an abrupt downshift in growth temperature. It leads to the increased production of the major cold-shock proteins, CS7.4 and CspB, respectively. CS7.4 is a transcriptional activator of two genes. CS7.4 and CspB share 43 per cent sequence identity with the nucleic acid-binding domain of the eukaryotic gene-regulatory Y-box factors. This cold-shock domain is conserved from bacteria to man and contains the RNA-binding RNP1 sequence motif. As a prototype of the cold-shock domain, the structure of CspB has been determined here from two crystal forms. In both, CspB is present as an antiparallel five-stranded beta-barrel. Three consecutive beta-strands, the central one containing the RNP1 motif, create a surface rich in aromatic and basic residues that are presumably involved in nucleic acid binding. Preferential binding of CspB to single-stranded DNA is observed in gel retardation experiments.

• Schnuchel A et al.
• Structure in solution of the major cold-shock protein from Bacillus subtilis.
• Nature. 1993; 364: 169-71

The cold-shock domain (CSD) is found in many eukaryotic transcriptional factors and is responsible for the specific binding to DNA of a cis-element called the Y-box. The same domain exists in the sequence of the Xenopus RNA-binding proteins FRG Y1 and FRG Y2 (refs 1, 3). The major cold-shock proteins of Escherichia coli (CS7.4) and B. subtilis (CspB) have sequences that are more than 40 per cent identical to the cold-shock domain. We present here the three-dimensional structure of CspB determined by nuclear magnetic resonance spectroscopy. The 67-residue protein consists of an antiparallel five-stranded beta-barrel with strands connected by turns and loops. The structure resembles that of staphylococcal nuclease and the gene-5 single-stranded-DNA-binding protein. A three-stranded beta-sheet, which contains the conserved RNA-binding motif RNP1 as well as a motif similar to RNP2 in two neighbouring antiparallel beta-strands, has basic and aromatic residues at its surface which could serve as a binding site for single-stranded DNA. CspB binds to single-stranded DNA in gel retardation experiments.

• Jones PG, VanBogelen RA, Neidhardt FC
• Induction of proteins in response to low temperature in Escherichia coli.
• J Bacteriol. 1987; 169: 2092-5

When the growth temperature of an exponential culture of Escherichia coli is abruptly decreased from 37 to 10 degrees C, growth stops for several hours before a new rate of growth is established. During this growth lag the number of proteins synthesized is dramatically reduced, and at one point only about two dozen proteins are made; 13 of these are made at differential rates that are 3 to 300 times increased over the rates at 37 degrees C. The protein with the highest rate of synthesis during the lag is not detectably made at 37 degrees C. The identities of several of these cold shock proteins correlate with previous observations that indicate a block in translation initiation at low temperatures.

Metabolism (metabolic pathways involving proteins which contain this domain)

% proteins involved	KEGG pathway ID	Description
54.55	map04530	Tight junction
9.09	map00260	Glycine, serine and threonine metabolism
9.09	map00970	Aminoacyl-tRNA biosynthesis
9.09	map00670	One carbon pool by folate
9.09	map00271	Methionine metabolism
9.09	map00300	Lysine biosynthesis

This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with CSP domain which could be assigned to a KEGG orthologous group, and not all proteins containing CSP domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

Structure (3D structures containing this domain)

3D Structures of CSP domains in PDB

PDB code	Title
1a62	CRYSTAL STRUCTURE OF THE RNA-BINDING DOMAIN OF THE TRANSCRIPTIONAL TERMINATOR PROTEIN RHO
1a63	THE NMR STRUCTURE OF THE RNA BINDING DOMAIN OF E.COLI RHO FACTOR SUGGESTS POSSIBLE RNA-PROTEIN INTERACTIONS, 10 STRUCTURES
1a8v	STRUCTURE OF THE RNA-BINDING DOMAIN OF THE RHO TRANSCRIPTION TERMINATOR
1c9o	CRYSTAL STRUCTURE ANALYSIS OF THE BACILLUS CALDOLYTICUS COLD SHOCK PROTEIN BC-CSP
1csp	CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS MAJOR COLD SHOCK PROTEIN, CSPB: A UNIVERSAL NUCLEIC-ACID BINDING DOMAIN
1csq	CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS MAJOR COLD SHOCK PROTEIN, CSPB: A UNIVERSAL NUCLEIC-ACID BINDING DOMAIN
1g6p	SOLUTION NMR STRUCTURE OF THE COLD SHOCK PROTEIN FROM THE HYPERTHERMOPHILIC BACTERIUM THERMOTOGA MARITIMA
1h95	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)
1hz9	BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY
1hza	BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY
1hzb	BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY
1hzc	BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY
1i5f	BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY
1mjc	CRYSTAL STRUCTURE OF CSPA, THE MAJOR COLD SHOCK PROTEIN OF ESCHERICHIA COLI
1nmf	MAJOR COLD-SHOCK PROTEIN, NMR, 20 STRUCTURES
1nmg	MAJOR COLD-SHOCK PROTEIN, NMR, MINIMIZED AVERAGE STRUCTURE
1pv4	X-ray crystal structure of the Rho transcription termination factor in complex with single stranded DNA
1pvo	X-ray crystal structure of Rho transcription termination factor in complex with ssRNA substrate and ANPPNP
1wfq	Solution structure of the first cold-shock domain of the human KIAA0885 protein (UNR protein)
1x65	Solution structure of the third cold-shock domain of the human KIAA0885 protein (UNR PROTEIN)
1xpo	Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin
1xpr	Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic 5a-formylbicyclomycin (FB)
1xpu	Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic 5a-(3-formylphenylsulfanyl)-dihydrobicyclomycin (FPDB)
2a8v	RHO TRANSCRIPTION TERMINATION FACTOR/RNA COMPLEX
2bh8	Combinatorial Protein 1b11
2es2	Crystal Structure Analysis of the Bacillus Subtilis Cold Shock Protein Bs-CspB in Complex with Hexathymidine
2f52	Solution structure of cold shock protein CspB from Bacillus subtilis in complex with heptathymidine
2hax	Crystal structure of Bacillus caldolyticus cold shock protein in complex with hexathymidine
2ht1	The closed ring structure of the Rho transcription termination factor in complex with nucleic acid in the motor domains
2i5l	Crystal structure of Bacillus subtilis Cold Shock Protein variant Bs-CspB M1R/E3K/K65I
2i5m	Crystal structure of Bacillus subtilis cold shock protein CspB variant A46K S48R
2id0	Escherichia coli RNase II
2ix0	RNase II
2ix1	RNase II D209N mutant
2k5n	Solution NMR Structure of the N-Terminal Domain of Protein ECA1580 from Erwinia carotovora, Northeast Structural Genomics Consortium Target EwR156A
2kcm	Solution NMR structure of the N-terminal OB-domain of SO_1732 from Shewanella oneidensis. Northeast Structural Genomics Consortium Target SoR210A.
2l15	Solution Structure of Cold Shock Protein CspA Using Combined NMR and CS-Rosetta method
2lss	Solution structure of the R. rickettsii cold shock-like protein
2lxj	Backbone 1H, 13C, and 15N Chemical Shift Assignments for cold shock protein, LmCsp with dT7
2lxk	Backbone 1H, 13C, and 15N Chemical Shift Assignments for cold shock protein, LmCsp
2mo0	2MO0
2mo1	2MO1
2mqh	2MQH
2n49	2N49
2ytv	Solution structure of the fifth cold-shock domain of the human KIAA0885 protein (unr protein)
2ytx	Solution structure of the second cold-shock domain of the human KIAA0885 protein (UNR protein)
2yty	Solution structure of the fourth cold-shock domain of the human KIAA0885 protein (UNR protein)
3a0j	Crystal structure of cold shock protein 1 from Thermus thermophilus HB8
3aqq	Crystal structure of human CRHSP-24
3cam	Crystal structure of the cold shock domain protein from Neisseria meningitidis
3i2z	Structure of cold shock protein E from Salmonella typhimurium
3ice	Rho transcription termination factor bound to RNA and ADP-BeF3
3l0o	Structure of RNA-free Rho transcription termination factor from Thermotoga maritima
3mef	MAJOR COLD-SHOCK PROTEIN FROM ESCHERICHIA COLI SOLUTION NMR STRUCTURE
3pf4	Crystal structure of Bs-CspB in complex with r(GUCUUUA)
3pf5	Crystal structure of Bs-CspB in complex with rU6
3trz	Mouse Lin28A in complex with let-7d microRNA pre-element
3ts0	Mouse Lin28A in complex with let-7f-1 microRNA pre-element
3ts2	Mouse Lin28A in complex with let-7g microRNA pre-element
3ulj	Crystal structure of apo Lin28B cold shock domain
4a4i	Crystal structure of the human Lin28b cold shock domain
4a75	The Lin28b Cold shock domain in complex with hexathymidine.
4a76	The Lin28b Cold shock domain in complex with heptathymidine
4alp	The Lin28b Cold shock domain in complex with hexauridine
4qqb	4QQB
5jji	5JJI
5jjk	5JJK
5jjl	5JJL

Links (links to other resources describing this domain)

• PFAM: CSD
• INTERPRO: IPR011129
• PROSITE: COLD_SHOCK