› 4yhz

X-ray diffraction
2.3Å resolution

Crystal structure of 304M3-B Fab in complex with H3K4me3 peptide

Released:
DOI: 10.2210/pdb4yhz/pdb
PDB entry 4yhz coloured by chain, front view.
PDB entry 4yhz coloured by chain, side view.
PDB entry 4yhz coloured by chain, top view.
Source organisms:
Primary publication:
Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation.
Hattori T, Lai D, Dementieva IS, Montaño SP, Kurosawa K, Zheng Y, Akin LR, Świst-Rosowska KM, Grzybowski AT, Koide A, Krajewski K, Strahl BD, Kelleher NL, Ruthenburg AJ, Koide S
Proc Natl Acad Sci U S A 113 2092-7 (2016)
PMID: 26862167

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-229986 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Fab Heavy Chain Chain: H
Molecule details ›
Chain: H
Length: 229 amino acids
Theoretical weight: 24.79 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Fab Light Chain Chain: L
Molecule details ›
Chain: L
Length: 215 amino acids
Theoretical weight: 23.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Histone H3.1 Chain: P
Molecule details ›
Chain: P
Length: 12 amino acids
Theoretical weight: 1.35 KDa
Source organism: synthetic construct
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-13; Coverage: 9%)
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 GOL 7 x GOL
Ligand SO4 1 x SO4
1 modified residue:
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P3121
Unit cell:
a: 130.375Å b: 130.375Å c: 96.365Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.184 0.183 0.213
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Next-generation antibodies for post-translational modifications.
Hattori et al. (2018)
4 more

1 mention without citation

Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation.
Hattori et al. (2016)