› 7f3i

X-ray diffraction
2.25Å resolution

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P212121

Released:
DOI: 10.2210/pdb7f3i/pdb
PDB entry 7f3i coloured by chain, front view.
PDB entry 7f3i coloured by chain, side view.
PDB entry 7f3i coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Zhang Y, Huang Y

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195160 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Y-box-binding protein 2 Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 93 amino acids
Theoretical weight: 10.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y2T7 (Residues: 85-177; Coverage: 26%)
Gene names: CSDA3, MSY2, YBX2
Sequence domains: 'Cold-shock' DNA-binding domain
RNA (5'-R(*GP*UP*(5MC)P*CP*(5MC))-3') Chains: B, D
Molecule details ›
Chains: B, D
Length: 5 nucleotides
Theoretical weight: 1.55 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 5MC 4 x 5MC

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P212121
Unit cell:
a: 43.532Å b: 59.348Å c: 118.623Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.185 0.246
Expression systems:
  • Escherichia coli
  • Not provided

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