› 5wyi

X-ray diffraction
2Å resolution

The Yaf9 YEATS domain Recognizing H3K122suc Peptide

Released:
DOI: 10.2210/pdb5wyi/pdb
PDB entry 5wyi coloured by chain, front view.
PDB entry 5wyi coloured by chain, side view.
PDB entry 5wyi coloured by chain, top view.
Source organisms:
Entry authors: Wang Y, Hao Q

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109880 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Protein AF-9 homolog Chain: A
Molecule details ›
Chain: A
Length: 165 amino acids
Theoretical weight: 18.98 KDa
Source organism: Saccharomyces cerevisiae RM11-1a
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
UniProt:
  • Canonical: B3LNW5 (Residues: 8-169; Coverage: 72%)
Gene names: SCRG_03242, YAF9
Sequence domains: YEATS family
Structure domains: YEATS domain
Protein AF-9 homolog Chains: B, C
Molecule details ›
Chains: B, C
Length: 164 amino acids
Theoretical weight: 18.92 KDa
Source organism: Saccharomyces cerevisiae RM11-1a
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
UniProt:
  • Canonical: B3LNW5 (Residues: 8-169; Coverage: 72%)
Gene names: SCRG_03242, YAF9
Sequence domains: YEATS family
Structure domains: YEATS domain
Histone H3.1 Chain: E
Molecule details ›
Chain: E
Length: 8 amino acids
Theoretical weight: 958 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 120-127; Coverage: 6%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

2 bound ligands:
Ligand SLL 1 x SLL
Ligand SIN 1 x SIN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P3
Unit cell:
a: 136.932Å b: 136.932Å c: 26.168Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.203 0.201 0.226
Expression systems:
  • Escherichia coli-Pichia pastoris shuttle vector pPpARG4
  • Not provided

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