› 8hl7

X-ray diffraction
2.8Å resolution

Crystal structure of p97 N/D1 in complex with a valosin-containing protein methyltransferase

Released:
DOI: 10.2210/pdb8hl7/pdb
PDB entry 8hl7 coloured by chain, front view.
PDB entry 8hl7 coloured by chain, side view.
PDB entry 8hl7 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for recognition and methylation of p97 by METTL21D, a valosin-containing protein lysine methyltransferase.
Nguyen TQ, Koh S, Kwon J, Jang S, Kang W, Yang JK
iScience 26 107222 (2023)
PMID: 37456834

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-273905 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protein N-lysine methyltransferase METTL21D Chain: A
Molecule details ›
Chain: A
Length: 208 amino acids
Theoretical weight: 23.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H867 (Residues: 16-222; Coverage: 90%)
Gene names: C14orf138, METTL21D, VCPKMT
Sequence domains: Lysine methyltransferase
Transitional endoplasmic reticulum ATPase Chain: B
Molecule details ›
Chain: B
Length: 436 amino acids
Theoretical weight: 48.79 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P55072 (Residues: 23-458; Coverage: 54%)
Gene names: HEL-220, HEL-S-70, VCP
Sequence domains:

Ligands and Environments

6 bound ligands:
Ligand SAH 1 x SAH
Ligand GOL 3 x GOL
Ligand FMT 2 x FMT
Ligand ACT 1 x ACT
Ligand ADP 1 x ADP
Ligand EPE 1 x EPE
1 modified residue:
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 5C (4A)
Spacegroup: P43212
Unit cell:
a: 60.78Å b: 60.78Å c: 473.91Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.217 0.261
Expression system: Escherichia coli

Quick links