› 7cna

X-ray diffraction
1.6Å resolution

Crystal structure of Spindlin1/C11orf84 complex bound to histone H3K4me3K9me3 peptide

Released:
DOI: 10.2210/pdb7cna/pdb
PDB entry 7cna coloured by chain, front view.
PDB entry 7cna coloured by chain, side view.
PDB entry 7cna coloured by chain, top view.
Source organisms:
Primary publication:
Structural mechanism of bivalent histone H3K4me3K9me3 recognition by the Spindlin1/C11orf84 complex in rRNA transcription activation.
Du Y, Yan Y, Xie S, Huang H, Wang X, Ng RK, Zhou MM, Qian C
OpenAccess logo Nat Commun 12 949 (2021)
PMID: 33574238

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-168125 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Spindlin-1 Chains: A, D
Molecule details ›
Chains: A, D
Length: 212 amino acids
Theoretical weight: 24.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y657 (Residues: 51-262; Coverage: 81%)
Gene names: OCR, SPIN, SPIN1
Sequence domains: Spin/Ssty Family
Spindlin interactor and repressor of chromatin-binding protein Chains: B, E
Molecule details ›
Chains: B, E
Length: 30 amino acids
Theoretical weight: 3.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9BUA3 (Residues: 254-283; Coverage: 8%)
Gene names: C11orf84, SPINDOC
ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-M3L-SER-THR Chain: C
Molecule details ›
Chain: C
Length: 12 amino acids
Theoretical weight: 1.39 KDa
Source organism: synthetic construct
Expression system: Not provided
ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-M3L-SER-GLY Chain: F
Molecule details ›
Chain: F
Length: 12 amino acids
Theoretical weight: 1.35 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand BEN 6 x BEN
Ligand CL 3 x CL
Ligand GOL 1 x GOL
1 modified residue:
Ligand M3L 4 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 45.603Å b: 101.184Å c: 56.615Å
α: 90° β: 91.41° γ: 90°
R-values:
R R work R free
0.173 0.172 0.201
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 citation in other articles

Real-time imaging of RNA polymerase I activity in living human cells.
Fu et al. (2023)
4 more

1 mention without citation

Catching Nucleosome by Its Decorated Tails Determines Its Functional States.
Sehrawat et al. (2022)