› 5tdw

X-ray diffraction
1.7Å resolution

Set3 PHD finger in complex with histone H3K4me3

Released:
DOI: 10.2210/pdb5tdw/pdb
PDB entry 5tdw coloured by chain, front view.
PDB entry 5tdw coloured by chain, side view.
PDB entry 5tdw coloured by chain, top view.
Source organisms:
Primary publication:
Structural Insight into Recognition of Methylated Histone H3K4 by Set3.
Gatchalian J, Ali M, Andrews FH, Zhang Y, Barrett AS, Kutateladze TG
J Mol Biol 429 2066-2074 (2017)
PMID: 27697561

Function and Biology Details

Biochemical function:
  • not assigned
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-153129 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
SET domain-containing protein 3 Chain: A
Molecule details ›
Chain: A
Length: 69 amino acids
Theoretical weight: 7.91 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P36124 (Residues: 116-184; Coverage: 9%)
Gene names: SET3, YKR029C
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Histone H3.1 Chain: B
Molecule details ›
Chain: B
Length: 11 amino acids
Theoretical weight: 1.29 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-12; Coverage: 8%)
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 ZN 2 x ZN
Ligand NA 1 x NA
1 modified residue:
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Unit cell:
a: 25.87Å b: 43.68Å c: 85.06Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 0.164 0.199
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

SET domains and stress: uncovering new functions for yeast Set4.
Tran et al. (2019)
4 other articles

5 mentions without citation

Structural Insight into Recognition of Methylated Histone H3K4 by Set3.
Gatchalian et al. (2017)
4 more