PDBsum entry 1h95

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Translation factor PDB id
Jmol PyMol
Protein chain
79 a.a. *
* Residue conservation analysis
PDB id:
Name: Translation factor
Title: 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)
Structure: Y-box binding protein. Chain: a. Fragment: cold shock domain. Synonym: csd. Engineered: yes. Other_details: single stranded DNA binding cold shock domain(csd) of human y-box protein 1 (yb-1)
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008.
NMR struc: 10 models
Authors: C.P.A.M.Kloks,C.A.E.M.Spronk,A.Hoffmann,G.W.Vuister, S.Grzesiek,C.W.Hilbers
Key ref:
C.P.Kloks et al. (2002). The solution structure and DNA-binding properties of the cold-shock domain of the human Y-box protein YB-1. J Mol Biol, 316, 317-326. PubMed id: 11851341 DOI: 10.1006/jmbi.2001.5334
23-Feb-01     Release date:   21-Feb-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P67809  (YBOX1_HUMAN) -  Nuclease-sensitive element-binding protein 1
324 a.a.
79 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     nucleic acid binding     2 terms  


DOI no: 10.1006/jmbi.2001.5334 J Mol Biol 316:317-326 (2002)
PubMed id: 11851341  
The solution structure and DNA-binding properties of the cold-shock domain of the human Y-box protein YB-1.
C.P.Kloks, C.A.Spronk, E.Lasonder, A.Hoffmann, G.W.Vuister, S.Grzesiek, C.W.Hilbers.
The human Y-box protein 1 (YB-1) is a member of the Y-box protein family, a class of proteins involved in transcriptional and translational regulation of a wide range of genes. Here, we report the solution structure of the cold-shock domain (CSD) of YB-1, which is thought to be responsible for nucleic acid binding. It is the first structure solved of a eukaryotic member of the cold-shock protein family and consists of a closed five-stranded anti-parallel beta-barrel capped by a long flexible loop. The structure of CSD is similar to the OB-fold and a comparison with bacterial cold-shock proteins shows that its structural properties are conserved from bacteria to man. Our data suggest the presence of a DNA-binding site consisting of a patch of positively charged and aromatic residues on the surface of the beta-barrel. Further, it is shown that CSD, which has a preference for binding single-stranded pyrimidine-rich sequences, binds weakly and hardly specifically to DNA. Binding affinities reported for intact YB-1 indicate that domains other than the CSD play a role in DNA binding of YB-1.
  Selected figure(s)  
Figure 2.
Figure 2. Toplogy of the b-barrel of YB-1 CSD. Observed NOEs typical of an anti-parallel b-sheet are indicated as entire arrows and in the case of overlap as broken-line arrows. Hydrogen bonds are indicated by hatched bars. Resi- dues that could not be observed in 1 H, 15 N-HSQC spectra are in gray boxes, proline residues are depicted in gray ovals. The b1 to b5 sheets comprise residues 3-17, 22-28, 31-37, 57-66 and 69-76, respectively. b-Bulges are present at residues 7-8, 14-15 and 73-74. Strand 5 is repeated at the bottom to illustrate the parallel closure of the barrel.
Figure 3.
Figure 3. (a) Ribbon diagram of the lowest energy structure of CSD. (b) Stereo view of an ensemble of ten refined structures superimposed for residues 6-13, 23-41, 57-65 and 69-77. Flexible loops are indicated in red (b3-b4) orange (b4-b5) and yellow (b1-b2). Loop b2-b3 (light blue) has a fixed orientation with respect to the core. The N and C ter- mini are shown in light green and white, respectively.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 316, 317-326) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20213426 A.K.Goroncy, S.Koshiba, N.Tochio, T.Tomizawa, M.Inoue, S.Watanabe, T.Harada, A.Tanaka, O.Ohara, T.Kigawa, and S.Yokoyama (2010).
The NMR solution structures of the five constituent cold-shock domains (CSD) of the human UNR (upstream of N-ras) protein.
  J Struct Funct Genomics, 11, 181-188.
PDB codes: 1wfq 1x65 2ytv 2ytx 2yty
20091748 M.Mihailovich, C.Militti, T.Gabaldón, and F.Gebauer (2010).
Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression.
  Bioessays, 32, 109-118.  
20529341 M.S.Clark, M.A.Thorne, F.A.Vieira, J.C.Cardoso, D.M.Power, and L.S.Peck (2010).
Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing.
  BMC Genomics, 11, 362.  
20331432 O.M.Selivanova, S.G.Guryanov, G.A.Enin, M.A.Skabkin, L.P.Ovchinnikov, and I.N.Serdyuk (2010).
YB-1 is capable of forming extended nanofibrils.
  Biochemistry (Mosc), 75, 115-120.  
20636440 R.Petruzzelli, S.Gaudino, G.Amendola, R.Sessa, S.Puzone, R.Di Concilio, G.d'Urzo, M.Amendolara, P.Izzo, and M.Grosso (2010).
Role of the cold shock domain protein A in the transcriptional regulation of HBG expression.
  Br J Haematol, 150, 689-699.  
  20944206 S.S.Krishna, L.Aravind, C.Bakolitsa, J.Caruthers, D.Carlton, M.D.Miller, P.Abdubek, T.Astakhova, H.L.Axelrod, H.J.Chiu, T.Clayton, M.C.Deller, L.Duan, J.Feuerhelm, J.C.Grant, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, A.Kumar, D.Marciano, D.McMullan, A.T.Morse, E.Nigoghossian, L.Okach, R.Reyes, C.L.Rife, H.van den Bedem, D.Weekes, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1160-1166.
PDB code: 3irb
19299548 C.Bousquet-Antonelli, and J.M.Deragon (2009).
A comprehensive analysis of the La-motif protein superfamily.
  RNA, 15, 750-764.  
19556243 M.H.Kim, K.Sasaki, and R.Imai (2009).
Cold shock domain protein 3 regulates freezing tolerance in Arabidopsis thaliana.
  J Biol Chem, 284, 23454-23460.  
19836337 T.Wang, H.Li, G.Lin, C.Tang, D.Li, C.Nathan, K.H.Darwin, and H.Li (2009).
Structural insights on the Mycobacterium tuberculosis proteasomal ATPase Mpa.
  Structure, 17, 1377-1385.
PDB code: 3fp9
17704806 A.G.Bader, and P.K.Vogt (2008).
Phosphorylation by Akt disables the anti-oncogenic activity of YB-1.
  Oncogene, 27, 1179-1182.  
18793384 K.G.Chernov, A.Mechulam, N.V.Popova, D.Pastre, E.S.Nadezhdina, O.V.Skabkina, N.A.Shanina, V.D.Vasiliev, A.Tarrade, J.Melki, V.Joshi, S.Baconnais, F.Toma, L.P.Ovchinnikov, and P.A.Curmi (2008).
YB-1 promotes microtubule assembly in vitro through interaction with tubulin and microtubules.
  BMC Biochem, 9, 23.  
18684830 R.Gorchakov, N.Garmashova, E.Frolova, and I.Frolov (2008).
Different types of nsP3-containing protein complexes in Sindbis virus-infected cells.
  J Virol, 82, 10088-10101.  
17545280 L.Giaquinto, P.M.Curmi, K.S.Siddiqui, A.Poljak, E.DeLong, S.DasSarma, and R.Cavicchioli (2007).
Structure and function of cold shock proteins in archaea.
  J Bacteriol, 189, 5738-5748.  
15806160 B.W.Sutherland, J.Kucab, J.Wu, C.Lee, M.C.Cheang, E.Yorida, D.Turbin, S.Dedhar, C.Nelson, M.Pollak, H.Leighton Grimes, K.Miller, S.Badve, D.Huntsman, C.Blake-Gilks, M.Chen, C.J.Pallen, and S.E.Dunn (2005).
Akt phosphorylates the Y-box binding protein 1 at Ser102 located in the cold shock domain and affects the anchorage-independent growth of breast cancer cells.
  Oncogene, 24, 4281-4292.  
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.  
16156790 R.Hofweber, G.Horn, T.Langmann, J.Balbach, W.Kremer, G.Schmitz, and H.R.Kalbitzer (2005).
The influence of cold shock proteins on transcription and translation studied in cell-free model systems.
  FEBS J, 272, 4691-4702.  
16258830 S.B.Nabuurs, E.Krieger, C.A.Spronk, A.J.Nederveen, G.Vriend, and G.W.Vuister (2005).
Definition of a new information-based per-residue quality parameter.
  J Biomol NMR, 33, 123-134.  
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.  
15039576 R.Bienert, M.Zeeb, L.Dostál, A.Feske, C.Magg, K.Max, H.Welfle, J.Balbach, and U.Heinemann (2004).
Single-stranded DNA bound to bacterial cold-shock proteins: preliminary crystallographic and Raman analysis.
  Acta Crystallogr D Biol Crystallogr, 60, 755-757.  
14530393 A.G.Bader, K.A.Felts, N.Jiang, H.W.Chang, and P.K.Vogt (2003).
Y box-binding protein 1 induces resistance to oncogenic transformation by the phosphatidylinositol 3-kinase pathway.
  Proc Natl Acad Sci U S A, 100, 12384-12389.  
12815724 K.Kohno, H.Izumi, T.Uchiumi, M.Ashizuka, and M.Kuwano (2003).
The pleiotropic functions of the Y-box-binding protein, YB-1.
  Bioessays, 25, 691-698.  
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.  
14732928 R.L.Rich, and D.G.Myszka (2003).
A survey of the year 2002 commercial optical biosensor literature.
  J Mol Recognit, 16, 351-382.  
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 codes are shown on the right.