5YTV Rna Binding Protein Rna date Nov 20, 2017
title Crystal Structure Of Yb1 Cold-Shock Domain In Complex With U
authors X.Yang, Y.Huang
compound source
Molecule: Nuclease-Sensitive Element-Binding Protein 1
Chain: A
Synonym: Ccaat-Binding Transcription Factor I Subunit A,Cbf Binding Protein B,Dbpb,Enhancer Factor I Subunit A,Efi-A,Y- Transcription Factor,Y-Box-Binding Protein 1,Yb-1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ybx1, Nsep1, Yb1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna (5'-R(Pupcpapupcpu)-3')
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 62
R_factor 0.196 R_Free 0.228
length a length b length c angle alpha angle beta angle gamma
66.275 66.275 35.195 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.70 Å

Primary referenceCrystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA., Yang XJ, Zhu H, Mu SR, Wei WJ, Yuan X, Wang M, Liu Y, Hui J, Huang Y, J Biol Chem. 2019 Jun 3. pii: RA119.007545. doi: 10.1074/jbc.RA119.007545. PMID:31160337
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (19 Kb) [Save to disk]
  • Biological Unit Coordinates (5ytv.pdb1.gz) 15 Kb
  • CSU: Contacts of Structural Units for 5YTV
  • Structure Factors (67 Kb)
  • Retrieve 5YTV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YTV from S2C, [Save to disk]
  • View 5YTV in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5YTV
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5ytv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ytv_B] [5ytv_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YTV
  • Community annotation for 5YTV at PDBWiki (http://pdbwiki.org)

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