5YTS 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(Pcpupupc)-3')
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 62
R_factor 0.187 R_Free 0.227
length a length b length c angle alpha angle beta angle gamma
65.711 65.711 36.967 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.77 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] (20 Kb) [Save to disk]
  • Biological Unit Coordinates (5yts.pdb1.gz) 16 Kb
  • CSU: Contacts of Structural Units for 5YTS
  • Structure Factors (61 Kb)
  • Retrieve 5YTS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YTS from S2C, [Save to disk]
  • View 5YTS 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 5YTS
  • 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 5yts from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5yts_A] [5yts_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YTS
  • Community annotation for 5YTS at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science