› 6a6l

X-ray diffraction
1.78Å resolution

Crystal structure of the cold shock domain of YB-1 in complex with m5C RNA

Released:
DOI: 10.2210/pdb6a6l/pdb
PDB entry 6a6l coloured by chain, front view.
PDB entry 6a6l coloured by chain, side view.
PDB entry 6a6l coloured by chain, top view.
Source organism: Homo sapiens
Entry author: Huang Y

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-159238 (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
RNA (5'-R(P*CP*AP*UP*(5MC))-3') Chain: D
Molecule details ›
Chain: D
Length: 6 nucleotides
Theoretical weight: 1.83 KDa
Source organism: Homo sapiens
Expression system: synthetic construct

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 5MC 1 x 5MC

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P62
Unit cell:
a: 66.38Å b: 66.38Å c: 34.702Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.183 0.18 0.207
Expression systems:
  • Escherichia coli
  • synthetic construct

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