› 5ytv

X-ray diffraction
1.7Å resolution

Crystal structure of YB1 cold-shock domain in complex with UCAUCU

Released:
DOI: 10.2210/pdb5ytv/pdb
PDB entry 5ytv coloured by chain, front view.
PDB entry 5ytv coloured by chain, side view.
PDB entry 5ytv coloured by chain, top view.
Source organisms:
Primary publication:
Crystal 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 294 10998-11010 (2019)
PMID: 31160337

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159235 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Y-box-binding protein 1 Chain: A
Molecule details ›
Chain: A
Length: 83 amino acids
Theoretical weight: 9 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P67809 (Residues: 50-130; Coverage: 25%)
Gene names: NSEP1, YB1, YBX1
Sequence domains: 'Cold-shock' DNA-binding domain
Structure domains: Nucleic acid-binding proteins
RNA (5'-R(P*UP*CP*AP*UP*CP*U)-3') Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P62
Unit cell:
a: 66.275Å b: 66.275Å c: 35.195Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.199 0.196 0.228
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

Structural Features of Tight-Junction Proteins.
Heinemann et al. (2019)
7 more

3 mentions without citation

Cold-Shock Domains-Abundance, Structure, Properties, and Nucleic-Acid Binding.
Heinemann et al. (2021)
2 more