› 6sqo

X-ray diffraction
1.41Å resolution

Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub

Released:
DOI: 10.2210/pdb6sqo/pdb
Model geometry
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PDB entry 6sqo coloured by chain, front view.
PDB entry 6sqo coloured by chain, side view.
PDB entry 6sqo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for DNA damage-induced phosphoregulation of MDM2 RING domain.
Magnussen HM, Ahmed SF, Sibbet GJ, Hristova VA, Nomura K, Hock AK, Archibald LJ, Jamieson AG, Fushman D, Vousden KH, Weissman AM, Huang DT
OpenAccess logo Nat Commun 11 2094 (2020)
PMID: 32350255

Function and Biology Details

Reactions catalysed: 
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
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
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-158735 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase Mdm2 Chains: A, D
Molecule details ›
Chains: A, D
Length: 62 amino acids
Theoretical weight: 6.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00987 (Residues: 430-491; Coverage: 13%)
Gene name: MDM2
Sequence domains: Zinc finger, C3HC4 type (RING finger)
Ubiquitin-conjugating enzyme E2 D2 Chains: B, E
Molecule details ›
Chains: B, E
Length: 146 amino acids
Theoretical weight: 16.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62837 (Residues: 2-147; Coverage: 99%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin Chains: C, F

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand CL 4 x CL
Ligand NO3 2 x NO3
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P61
Unit cell:
a: 129.709Å b: 129.709Å c: 70.537Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.139 0.139 0.173
Expression system: Escherichia coli

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Citations

6 review citations

A unified model for the G1/S cell cycle transition.
Hume et al. (2020)
5 more

2 mentions without citation

Bivalent binding of p14ARF to MDM2 RING and acidic domains inhibits E3 ligase function.
Kowalczyk et al. (2022)
1 more

PDB-REDO

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