PDBe 5cvd

X-ray diffraction
1.3Å resolution

Crystal structure of human NRMT1 in complex with alpha-N-dimethylated human CENP-A peptide

Released:
Source organism: Homo sapiens
Primary publication:
Molecular basis for histone N-terminal methylation by NRMT1.
Genes Dev. (2015)
PMID: 26543159

Function and Biology Details

Reaction catalysed:
(1) 3 S-adenosyl-L-methionine + N-terminal-(A,S)PK-[protein] = 3 S-adenosyl-L-homocysteine + N-terminal-N,N,N-trimethyl-N-(A,S)PK-[protein] (overall reaction)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
N-terminal Xaa-Pro-Lys N-methyltransferase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 243 amino acids
Theoretical weight: 27.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BV86 (Residues: 1-223; Coverage: 100%)
Gene names: AD-003, C9orf32, METTL11A, NRMT, NRMT1, NTMT1
Sequence domains: AdoMet dependent proline di-methyltransferase
Structure domains: Vaccinia Virus protein VP39
Histone H3-like centromeric protein A Chains: D, E
Molecule details ›
Chains: D, E
Length: 9 amino acids
Theoretical weight: 1.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P49450 (Residues: 2-10; Coverage: 6%)
Gene name: CENPA

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2
Unit cell:
a: 114.839Å b: 66.245Å c: 68.998Å
α: 90° β: 106.69° γ: 90°
R-values:
R R work R free
0.133 0.132 0.16
Expression system: Escherichia coli BL21(DE3)