› 5mnj

X-ray diffraction
2.16Å resolution

Structure of MDM2-MDMX-UbcH5B-ubiquitin complex

Released:
DOI: 10.2210/pdb5mnj/pdb
PDB entry 5mnj coloured by chain, front view.
PDB entry 5mnj coloured by chain, side view.
PDB entry 5mnj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural analysis of MDM2 RING separates degradation from regulation of p53 transcription activity.
Nomura K, Klejnot M, Kowalczyk D, Hock AK, Sibbet GJ, Vousden KH, Huang DT
Nat Struct Mol Biol 24 578-587 (2017)
PMID: 28553961

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-127314 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Ubiquitin-conjugating enzyme E2 D2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 147 amino acids
Theoretical weight: 16.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin Chains: B, F
Molecule details ›
Chains: B, F
Length: 81 amino acids
Theoretical weight: 8.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
E3 ubiquitin-protein ligase Mdm2 Chains: C, G
Molecule details ›
Chains: C, G
Length: 86 amino acids
Theoretical weight: 9.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00987 (Residues: 428-491; Coverage: 13%)
Gene name: MDM2
Sequence domains: Zinc finger, C3HC4 type (RING finger)
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Protein Mdm4 Chains: D, H
Molecule details ›
Chains: D, H
Length: 64 amino acids
Theoretical weight: 7.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O15151 (Residues: 427-490; Coverage: 13%)
Gene names: MDM4, MDMX
Sequence domains: Zinc finger, C3HC4 type (RING finger)
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P1
Unit cell:
a: 54.24Å b: 62.76Å c: 66.35Å
α: 69.83° β: 69.22° γ: 78.21°
R-values:
R R work R free
0.192 0.19 0.231
Expression system: Escherichia coli

Quick links

Citations

2 review citations

How to Inactivate Human Ubiquitin E3 Ligases by Mutation.
Garcia-Barcena et al. (2020)
1 more

12 mentions without citation

Post-translational regulation of ubiquitin signaling.
Song et al. (2019)
11 more