› 5cve

X-ray diffraction
1.5Å resolution

Crystal Structure of human NRMT1 in complex with dimethylated fly H2B peptide and SAH

Released:
DOI: 10.2210/pdb5cve/pdb
PDB entry 5cve coloured by chain, front view.
PDB entry 5cve coloured by chain, side view.
PDB entry 5cve coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis for histone N-terminal methylation by NRMT1.
Wu R, Yue Y, Zheng X, Li H
Genes Dev 29 2337-42 (2015)
PMID: 26543159

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + N-terminal-(A,S)PK-[protein] = S-adenosyl-L-homocysteine + N-terminal-N-methyl-N-(A,S)PK-[protein]
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-135443 (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 H2B Chains: D, E
Molecule details ›
Chains: D, E
Length: 9 amino acids
Theoretical weight: 887 Da
Source organism: Drosophila melanogaster
Expression system: Not provided
UniProt:
  • Canonical: P02283 (Residues: 3-10; Coverage: 7%)
Gene names: CG17949, CG33868, CG33870, CG33872, CG33874, CG33876, CG33878, CG33880, CG33882, CG33884, CG33886, CG33888, CG33890, CG33892, CG33894, CG33896, CG33898, CG33900, CG33902, CG33904, CG33906, CG33908, CG33910, His2B, His2B:CG17949, His2B:CG33868, His2B:CG33870, His2B:CG33872, His2B:CG33874, His2B:CG33876, His2B:CG33878, His2B:CG33880, His2B:CG33882, His2B:CG33884, His2B:CG33886, His2B:CG33888, His2B:CG33890, His2B:CG33892, His2B:CG33894, His2B:CG33896, His2B:CG33898, His2B:CG33900, His2B:CG33902, His2B:CG33904, His2B:CG33906, His2B:CG33908, His2B:CG33910

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: 114.836Å b: 66.302Å c: 68.73Å
α: 90° β: 106.44° γ: 90°
R-values:
R R work R free
0.153 0.153 0.18
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

The upstreams and downstreams of H3K79 methylation by DOT1L.
Vlaming et al. (2016)
1 more

3 mentions without citation

Chemical Biology of Protein N-Terminal Methyltransferases.
Huang R. (2019)
2 more