PDBsum entry 1nmf

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Transcription regulation PDB id
Protein chain
67 a.a. *
* Residue conservation analysis
PDB id:
Name: Transcription regulation
Title: Major cold-shock protein, nmr, 20 structures
Structure: Major cold-shock protein. Chain: a. Synonym: cspb. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 20 models
Authors: A.Schnuchel,T.A.Holak
Key ref: A.Schnuchel et al. (1993). Structure in solution of the major cold-shock protein from Bacillus subtilis. Nature, 364, 169-171. PubMed id: 8321289
05-Feb-96     Release date:   11-Jul-96    
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Protein chain
Pfam   ArchSchema ?
P32081  (CSPB_BACSU) -  Cold shock protein CspB
67 a.a.
67 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     transcription, DNA-dependent   2 terms 
  Biochemical function     nucleic acid binding     2 terms  


Nature 364:169-171 (1993)
PubMed id: 8321289  
Structure in solution of the major cold-shock protein from Bacillus subtilis.
A.Schnuchel, R.Wiltscheck, M.Czisch, M.Herrler, G.Willimsky, P.Graumann, M.A.Marahiel, T.A.Holak.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21426380 N.Mojib, D.T.Andersen, and A.K.Bej (2011).
Structure and function of  a cold shock domain fold protein, CspD, in Janthinobacterium sp. Ant5-2 from East Antarctica.
  FEMS Microbiol Lett, 319, 106-114.  
21258851 S.Jain, B.Saluja, A.Gupta, S.S.Marla, and R.Goel (2011).
Validation of Arsenic Resistance in Bacillus cereus Strain AG27 by Comparative Protein Modeling of arsC Gene Product.
  Protein J, 30, 91.  
20020303 M.Khan, A.Kumar, and R.Goel (2010).
Comparative protein modeling, prediction of conserved residue and active sites in cold resistant protein isolated from CRPF(1), a cold tolerant mutant of Pseudomonas fluorescens.
  Curr Microbiol, 60, 428-434.  
19145605 A.L.Stewart, and M.L.Waters (2009).
Structural effects on ss- and dsDNA recognition by a beta-hairpin peptide.
  Chembiochem, 10, 539-544.  
19840122 S.Phadtare, and K.Severinov (2009).
Comparative analysis of changes in gene expression due to RNA melting activities of translation initiation factor IF1 and a cold shock protein of the CspA family.
  Genes Cells, 14, 1227-1239.  
18299294 C.D.Geierhaas, X.Salvatella, J.Clarke, and M.Vendruscolo (2008).
Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.
  Protein Eng Des Sel, 21, 215-222.  
  18391418 J.Ren, J.E.Nettleship, S.Sainsbury, N.J.Saunders, and R.J.Owens (2008).
Structure of the cold-shock domain protein from Neisseria meningitidis reveals a strand-exchanged dimer.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 247-251.
PDB code: 3cam
18424511 M.Sackewitz, S.von Einem, G.Hause, M.Wunderlich, F.X.Schmid, and E.Schwarz (2008).
A folded and functional protein domain in an amyloid-like fibril.
  Protein Sci, 17, 1044-1054.  
17266726 K.E.Max, M.Zeeb, R.Bienert, J.Balbach, and U.Heinemann (2007).
Common mode of DNA binding to cold shock domains. Crystal structure of hexathymidine bound to the domain-swapped form of a major cold shock protein from Bacillus caldolyticus.
  FEBS J, 274, 1265-1279.
PDB code: 2hax
17384193 S.Phadtare, T.Kazakov, M.Bubunenko, D.L.Court, T.Pestova, and K.Severinov (2007).
Transcription antitermination by translation initiation factor IF1.
  J Bacteriol, 189, 4087-4093.  
17088256 D.Johnston, C.Tavano, S.Wickner, and N.Trun (2006).
Specificity of DNA binding and dimerization by CspE from Escherichia coli.
  J Biol Chem, 281, 40208-40215.  
16956971 M.Zeeb, K.E.Max, U.Weininger, C.Löw, H.Sticht, and J.Balbach (2006).
Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution.
  Nucleic Acids Res, 34, 4561-4571.
PDB code: 2f52
16844745 X.Huang, and H.X.Zhou (2006).
Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics simulations.
  Biophys J, 91, 2451-2463.  
16955517 Y.Qiu, S.Kathariou, and D.M.Lubman (2006).
Proteomic analysis of cold adaptation in a Siberian permafrost bacterium--Exiguobacterium sibiricum 255-15 by two-dimensional liquid separation coupled with mass spectrometry.
  Proteomics, 6, 5221-5233.  
16084391 J.L.Arolas, L.D'Silva, G.M.Popowicz, F.X.Aviles, T.A.Holak, and S.Ventura (2005).
NMR structural characterization and computational predictions of the major intermediate in oxidative folding of leech carboxypeptidase inhibitor.
  Structure, 13, 1193-1202.
PDB codes: 1zfi 1zfl
16118215 M.Singh, M.Krajewski, A.Mikolajka, and T.A.Holak (2005).
Molecular determinants for the complex formation between the retinoblastoma protein and LXCXE sequences.
  J Biol Chem, 280, 37868-37876.  
15592429 P.Frankel, A.Aronheim, E.Kavanagh, M.S.Balda, K.Matter, T.D.Bunney, and C.J.Marshall (2005).
RalA interacts with ZONAB in a cell density-dependent manner and regulates its transcriptional activity.
  EMBO J, 24, 54-62.  
14739320 A.Jung, C.Bamann, W.Kremer, H.R.Kalbitzer, and E.Brunner (2004).
High-temperature solution NMR structure of TmCsp.
  Protein Sci, 13, 342-350.  
15326599 B.N.Dominy, H.Minoux, and C.L.Brooks (2004).
An electrostatic basis for the stability of thermophilic proteins.
  Proteins, 57, 128-141.  
12493834 M.Zeeb, and J.Balbach (2003).
Single-stranded DNA binding of the cold-shock protein CspB from Bacillus subtilis: NMR mapping and mutational characterization.
  Protein Sci, 12, 112-123.  
14531859 S.Phadtare, J.Hwang, K.Severinov, and M.Inouye (2003).
CspB and CspL, thermostable cold-shock proteins from Thermotoga maritima.
  Genes Cells, 8, 801-810.  
12493704 Y.Iuchi, T.Kaneko, S.Matsuki, I.Sasagawa, and J.Fujii (2003).
Concerted changes in the YB2/RYB-a protein and protamine 2 messenger RNA in the mouse testis under heat stress.
  Biol Reprod, 68, 129-135.  
11752341 M.H.Weber, I.Fricke, N.Doll, and M.A.Marahiel (2002).
CSDBase: an interactive database for cold shock domain-containing proteins and the bacterial cold shock response.
  Nucleic Acids Res, 30, 375-378.  
12171653 M.H.Weber, and M.A.Marahiel (2002).
Coping with the cold: the cold shock response in the Gram-positive soil bacterium Bacillus subtilis.
  Philos Trans R Soc Lond B Biol Sci, 357, 895-907.  
11861653 S.F.Falsone, M.Weichel, R.Crameri, M.Breitenbach, and A.J.Kungl (2002).
Unfolding and double-stranded DNA binding of the cold shock protein homologue Cla h 8 from Cladosporium herbarum.
  J Biol Chem, 277, 16512-16516.  
11260474 K.Yamanaka, W.Zheng, E.Crooke, Y.H.Wang, and M.Inouye (2001).
CspD, a novel DNA replication inhibitor induced during the stationary phase in Escherichia coli.
  Mol Microbiol, 39, 1572-1584.  
11717297 M.H.Weber, C.L.Beckering, and M.A.Marahiel (2001).
Complementation of cold shock proteins by translation initiation factor IF1 in vivo.
  J Bacteriol, 183, 7381-7386.  
11322871 W.Kremer, B.Schuler, S.Harrieder, M.Geyer, W.Gronwald, C.Welker, R.Jaenicke, and H.R.Kalbitzer (2001).
Solution NMR structure of the cold-shock protein from the hyperthermophilic bacterium Thermotoga maritima.
  Eur J Biochem, 268, 2527-2539.
PDB code: 1g6p
11376140 X.Manival, L.Ghisolfi-Nieto, G.Joseph, P.Bouvet, and M.Erard (2001).
RNA-binding strategies common to cold-shock domain- and RNA recognition motif-containing proteins.
  Nucleic Acids Res, 29, 2223-2233.  
11069676 N.Wang, K.Yamanaka, and M.Inouye (2000).
Acquisition of double-stranded DNA-binding ability in a hybrid protein between Escherichia coli CspA and the cold shock domain of human YB-1.
  Mol Microbiol, 38, 526-534.  
  9847309 C.E.Harris, R.A.Boden, and C.R.Astell (1999).
A novel heterogeneous nuclear ribonucleoprotein-like protein interacts with NS1 of the minute virus of mice.
  J Virol, 73, 72-80.  
  10048332 C.Welker, G.Böhm, H.Schurig, and R.Jaenicke (1999).
Cloning, overexpression, purification, and physicochemical characterization of a cold shock protein homolog from the hyperthermophilic bacterium Thermotoga maritima.
  Protein Sci, 8, 394-403.  
  10515936 K.Neuhaus, K.P.Francis, S.Rapposch, A.Görg, and S.Scherer (1999).
Pathogenic Yersinia species carry a novel, cold-inducible major cold shock protein tandem gene duplication producing both bicistronic and monocistronic mRNA.
  J Bacteriol, 181, 6449-6455.  
  10386885 M.Gross, D.K.Wilkins, M.C.Pitkeathly, E.W.Chung, C.Higham, A.Clark, and C.M.Dobson (1999).
Formation of amyloid fibrils by peptides derived from the bacterial cold shock protein CspB.
  Protein Sci, 8, 1350-1357.  
10074340 M.Jacob, G.Holtermann, D.Perl, J.Reinstein, T.Schindler, M.A.Geeves, and F.X.Schmid (1999).
Microsecond folding of the cold shock protein measured by a pressure-jump technique.
  Biochemistry, 38, 2882-2891.  
10559248 M.M.Lopez, K.Yutani, and G.I.Makhatadze (1999).
Interactions of the major cold shock protein of Bacillus subtilis CspB with single-stranded DNA templates of different base composition.
  J Biol Chem, 274, 33601-33608.  
10407144 P.Carmona, A.Rodríguez-Casado, and M.Molina (1999).
Conformational structure and binding mode of glyceraldehyde-3-phosphate dehydrogenase to tRNA studied by Raman and CD spectroscopy.
  Biochim Biophys Acta, 1432, 222-233.  
  10049359 S.L.Hunt, J.J.Hsuan, N.Totty, and R.J.Jackson (1999).
unr, a cellular cytoplasmic RNA-binding protein with five cold-shock domains, is required for internal initiation of translation of human rhinovirus RNA.
  Genes Dev, 13, 437-448.  
9920884 T.Schindler, P.L.Graumann, D.Perl, S.Ma, F.X.Schmid, and M.A.Marahiel (1999).
The family of cold shock proteins of Bacillus subtilis. Stability and dynamics in vitro and in vivo.
  J Biol Chem, 274, 3407-3413.  
9501917 D.Perl, C.Welker, T.Schindler, K.Schröder, M.A.Marahiel, R.Jaenicke, and F.X.Schmid (1998).
Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins.
  Nat Struct Biol, 5, 229-235.  
9646873 G.Varani, and K.Nagai (1998).
RNA recognition by RNP proteins during RNA processing.
  Annu Rev Biophys Biomol Struct, 27, 407-445.  
9757828 P.L.Graumann, and M.A.Marahiel (1998).
A superfamily of proteins that contain the cold-shock domain.
  Trends Biochem Sci, 23, 286-290.  
9365254 H.A.Thieringer, K.Singh, H.Trivedi, and M.Inouye (1997).
Identification and developmental characterization of a novel Y-box protein from Drosophila melanogaster.
  Nucleic Acids Res, 25, 4764-4770.  
9032054 M.A.Kercher, P.Lu, and M.Lewis (1997).
Lac repressor-operator complex.
  Curr Opin Struct Biol, 7, 76-85.  
9159122 M.Jacob, T.Schindler, J.Balbach, and F.X.Schmid (1997).
Diffusion control in an elementary protein folding reaction.
  Proc Natl Acad Sci U S A, 94, 5622-5627.  
9135158 M.Sette, P.van Tilborg, R.Spurio, R.Kaptein, M.Paci, C.O.Gualerzi, and R.Boelens (1997).
The structure of the translational initiation factor IF1 from E.coli contains an oligomer-binding motif.
  EMBO J, 16, 1436-1443.
PDB code: 1ah9
  8631682 B.Mayr, T.Kaplan, S.Lechner, and S.Scherer (1996).
Identification and purification of a family of dimeric major cold shock protein homologs from the psychrotrophic Bacillus cereus WSBC 10201.
  J Bacteriol, 178, 2916-2925.  
9035369 G.Parisi, J.Echave, D.Ghiringhelli, and V.Romanowski (1996).
Computational characterisation of potential RNA-binding sites in arenavirus nucleocapsid proteins.
  Virus Genes, 13, 247-254.  
8798444 K.Matsumoto, F.Meric, and A.P.Wolffe (1996).
Translational repression dependent on the interaction of the Xenopus Y-box protein FRGY2 with mRNA. Role of the cold shock domain, tail domain, and selective RNA sequence recognition.
  J Biol Chem, 271, 22706-22712.  
  8755892 P.Graumann, K.Schröder, R.Schmid, and M.A.Marahiel (1996).
Cold shock stress-induced proteins in Bacillus subtilis.
  J Bacteriol, 178, 4611-4619.  
8967899 P.Graumann, and M.A.Marahiel (1996).
A case of convergent evolution of nucleic acid binding modules.
  Bioessays, 18, 309-315.  
8988022 T.Schindler, and F.X.Schmid (1996).
Thermodynamic properties of an extremely rapid protein folding reaction.
  Biochemistry, 35, 16833-16842.  
7664117 I.W.Mattaj, and K.Nagai (1995).
Recruiting proteins to the RNA world.
  Nat Struct Biol, 2, 518-522.  
7476164 K.Schröder, P.Graumann, A.Schnuchel, T.A.Holak, and M.A.Marahiel (1995).
Mutational analysis of the putative nucleic acid-binding surface of the cold-shock domain, CspB, revealed an essential role of aromatic and basic residues in binding of single-stranded DNA containing the Y-box motif.
  Mol Microbiol, 16, 699-708.  
7746155 L.R.Kowalski, K.Kondo, and M.Inouye (1995).
Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae.
  Mol Microbiol, 15, 341-353.  
  7628456 M.Bycroft, S.Grünert, A.G.Murzin, M.Proctor, and D.St Johnston (1995).
NMR solution structure of a dsRNA binding domain from Drosophila staufen protein reveals homology to the N-terminal domain of ribosomal protein S5.
  EMBO J, 14, 3563-3571.
PDB code: 1stu
7541909 N.Sato (1995).
A family of cold-regulated RNA-binding protein genes in the cyanobacterium Anabaena variabilis M3.
  Nucleic Acids Res, 23, 2161-2167.  
7499328 P.Bouvet, K.Matsumoto, and A.P.Wolffe (1995).
Sequence-specific RNA recognition by the Xenopus Y-box proteins. An essential role for the cold shock domain.
  J Biol Chem, 270, 28297-28303.  
  7556054 R.H.Folmer, M.Nilges, R.N.Konings, and C.W.Hilbers (1995).
Solution structure of the single-stranded DNA binding protein of the filamentous Pseudomonas phage Pf3: similarity to other proteins binding to single-stranded nucleic acids.
  EMBO J, 14, 4132-4142.
PDB code: 1pfs
7628487 S.Kudo, M.G.Mattei, and M.Fukuda (1995).
Characterization of the gene for dbpA, a family member of the nucleic-acid-binding proteins containing a cold-shock domain.
  Eur J Biochem, 231, 72-82.  
7552728 T.Schindler, M.Herrler, M.A.Marahiel, and F.X.Schmid (1995).
Extremely rapid protein folding in the absence of intermediates.
  Nat Struct Biol, 2, 663-673.  
7565651 A.P.Stassen, R.H.Folmer, C.W.Hilbers, and R.N.Konings (1994).
Single-stranded DNA binding protein encoded by the filamentous bacteriophage M13: structural and functional characteristics.
  Mol Biol Rep, 20, 109-127.  
8031301 A.P.Wolffe (1994).
Structural and functional properties of the evolutionarily ancient Y-box family of nucleic acid binding proteins.
  Bioessays, 16, 245-251.  
  7920256 A.Teplyakov, G.Obmolova, K.S.Wilson, K.Ishii, H.Kaji, T.Samejima, and I.Kuranova (1994).
Crystal structure of inorganic pyrophosphatase from Thermus thermophilus.
  Protein Sci, 3, 1098-1107.
PDB code: 2prd
8044840 E.Fabre, W.C.Boelens, C.Wimmer, I.W.Mattaj, and E.C.Hurt (1994).
Nup145p is required for nuclear export of mRNA and binds homopolymeric RNA in vitro via a novel conserved motif.
  Cell, 78, 275-289.  
  7703860 G.I.Makhatadze, and M.A.Marahiel (1994).
Effect of pH and phosphate ions on self-association properties of the major cold-shock protein from Bacillus subtilis.
  Protein Sci, 3, 2144-2147.  
7518919 H.Jacquemin-Sablon, G.Triqueneaux, S.Deschamps, M.le Maire, J.Doniger, and F.Dautry (1994).
Nucleic acid binding and intracellular localization of unr, a protein with five cold shock domains.
  Nucleic Acids Res, 22, 2643-2650.  
8197194 H.Schindelin, W.Jiang, M.Inouye, and U.Heinemann (1994).
Crystal structure of CspA, the major cold shock protein of Escherichia coli.
  Proc Natl Acad Sci U S A, 91, 5119-5123.
PDB code: 1mjc
7984775 J.M.Valpuesta, and J.L.Carrascosa (1994).
Structure of viral connectors and their function in bacteriophage assembly and DNA packaging.
  Q Rev Biophys, 27, 107-155.  
8127704 J.Muñoz-Dorado, K.Kondo, M.Inouye, and H.Sone (1994).
Identification of cis- and trans-acting elements involved in the expression of cold shock-inducible TIP1 gene of yeast Saccharomyces cerevisiae.
  Nucleic Acids Res, 22, 560-568.  
7515185 K.Newkirk, W.Feng, W.Jiang, R.Tejero, S.D.Emerson, M.Inouye, and G.T.Montelione (1994).
Solution NMR structure of the major cold shock protein (CspA) from Escherichia coli: identification of a binding epitope for DNA.
  Proc Natl Acad Sci U S A, 91, 5114-5118.
PDB code: 1mef
7984109 K.Yamanaka, T.Mitani, T.Ogura, H.Niki, and S.Hiraga (1994).
Cloning, sequencing, and characterization of multicopy suppressors of a mukB mutation in Escherichia coli.
  Mol Microbiol, 13, 301-312.  
  8045252 M.Delarue, A.Poterszman, S.Nikonov, M.Garber, D.Moras, and J.C.Thierry (1994).
Crystal structure of a prokaryotic aspartyl tRNA-synthetase.
  EMBO J, 13, 3219-3229.  
7530842 M.Ladomery, and J.Sommerville (1994).
Binding of Y-box proteins to RNA: involvement of different protein domains.
  Nucleic Acids Res, 22, 5582-5589.  
8193307 N.Sato (1994).
A cold-regulated cyanobacterial gene cluster encodes RNA-binding protein and ribosomal protein S21.
  Plant Mol Biol, 24, 819-823.  
8022261 S.J.Lee, A.Xie, W.Jiang, J.P.Etchegaray, P.G.Jones, and M.Inouye (1994).
Family of the major cold-shock protein, CspA (CS7.4), of Escherichia coli, whose members show a high sequence similarity with the eukaryotic Y-box binding proteins.
  Mol Microbiol, 11, 833-839.  
8290338 E.Birney, S.Kumar, and A.R.Krainer (1993).
Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors.
  Nucleic Acids Res, 21, 5803-5816.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.