› 3u88

X-ray diffraction
3Å resolution

Crystal structure of human menin in complex with MLL1 and LEDGF

Released:
DOI: 10.2210/pdb3u88/pdb
PDB entry 3u88 coloured by chain, front view.
PDB entry 3u88 coloured by chain, side view.
PDB entry 3u88 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The same pocket in menin binds both MLL and JUND but has opposite effects on transcription.
Huang J, Gurung B, Wan B, Matkar S, Veniaminova NA, Wan K, Merchant JL, Hua X, Lei M
Nature 482 542-6 (2012)
PMID: 22327296

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-126200 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Menin Chains: A, B
Molecule details ›
Chains: A, B
Length: 550 amino acids
Theoretical weight: 61.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O00255 (Residues: 2-610; Coverage: 90%)
Gene names: MEN1, SCG2
Sequence domains: Menin
MLL cleavage product N320 Chains: M, N
Molecule details ›
Chains: M, N
Length: 75 amino acids
Theoretical weight: 7.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q03164 (Residues: 103-153; Coverage: 1%)
Gene names: ALL1, CXXC7, HRX, HTRX, KMT2A, MLL, MLL1, TRX1
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
PC4 and SFRS1-interacting protein Chains: C, D
Molecule details ›
Chains: C, D
Length: 89 amino acids
Theoretical weight: 10.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O75475 (Residues: 347-435; Coverage: 17%)
Gene names: DFS70, LEDGF, PSIP1, PSIP2
Sequence domains: Lens epithelium-derived growth factor (LEDGF)
Structure domains: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70

Ligands and Environments

5 bound ligands:
Ligand CHD 2 x CHD
Ligand GGB 5 x GGB
Ligand 0BR 2 x 0BR
Ligand GLV 6 x GLV
Ligand SO4 8 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P6122
Unit cell:
a: 187.99Å b: 187.99Å c: 238.417Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.205 0.202 0.233
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

53 review citations

Epigenetic modifications of histones in cancer.
Zhao et al. (2019)
52 more

10 mentions without citation

Multiple Endocrine Neoplasia Type 1: Latest Insights.
Brandi et al. (2021)
9 more