› 7kzr

Electron Microscopy
4.4Å resolution

Structure of the human Fanconi Anaemia Core-UBE2T-ID complex

Released:
DOI: 10.2210/pdb7kzr/pdb
PDB entry 7kzr coloured by chain, front view.
PDB entry 7kzr coloured by chain, side view.
PDB entry 7kzr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of the FA core ubiquitin ligase closing the ID clamp on DNA.
Wang S, Wang R, Peralta C, Yaseen A, Pavletich NP
Nat Struct Mol Biol 28 300-309 (2021)
PMID: 33686268
Related structures: EMD-23087

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

Structure analysis Details

Assembly composition:
hetero heptadecamer (preferred)
PDBe Complex ID:
PDB-CPX-110662 (preferred)
Entry contents:
12 distinct polypeptide molecules
Macromolecules (12 distinct):
Fanconi anemia group A protein Chains: A, S
Molecule details ›
Chains: A, S
Length: 1477 amino acids
Theoretical weight: 165.51 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O15360 (Residues: 1-1455; Coverage: 100%)
Gene names: FAA, FACA, FANCA, FANCH
Sequence domains:
Fanconi anemia group B protein Chains: B, O
Molecule details ›
Chains: B, O
Length: 884 amino acids
Theoretical weight: 100.64 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8NB91 (Residues: 1-859; Coverage: 100%)
Gene name: FANCB
Fanconi anemia group C protein Chain: C
Molecule details ›
Chain: C
Length: 583 amino acids
Theoretical weight: 66.29 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q00597 (Residues: 1-558; Coverage: 100%)
Gene names: FAC, FACC, FANCC
Sequence domains: Fanconi anaemia group C protein
Fanconi anemia group E protein Chain: E
Molecule details ›
Chain: E
Length: 555 amino acids
Theoretical weight: 61.03 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9HB96 (Residues: 1-536; Coverage: 100%)
Gene names: FACE, FANCE
Sequence domains: Fanconi Anaemia group E protein FANCE
Fanconi anemia group F protein Chain: F
Molecule details ›
Chain: F
Length: 399 amino acids
Theoretical weight: 45.11 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9NPI8 (Residues: 1-374; Coverage: 100%)
Gene name: FANCF
Sequence domains: Fanconi anemia group F protein (FANCF)
Fanconi anemia group G protein Chains: G, H
Molecule details ›
Chains: G, H
Length: 641 amino acids
Theoretical weight: 70.87 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O15287 (Residues: 1-622; Coverage: 100%)
Gene names: FANCG, XRCC9
E3 ubiquitin-protein ligase FANCL Chains: L, M
Molecule details ›
Chains: L, M
Length: 394 amino acids
Theoretical weight: 45.2 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9NW38 (Residues: 1-375; Coverage: 100%)
Gene names: FANCL, PHF9
Sequence domains:
Fanconi anemia core complex-associated protein 100 Chains: P, Q
Molecule details ›
Chains: P, Q
Length: 906 amino acids
Theoretical weight: 96.51 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q0VG06 (Residues: 1-881; Coverage: 100%)
Gene names: C17orf70, FAAP100
Sequence domains: Fanconi anemia-associated
Fanconi anemia core complex-associated protein 20 Chain: W
Molecule details ›
Chain: W
Length: 39 amino acids
Theoretical weight: 4.04 KDa
Source organism: Homo sapiens
Fanconi anemia, complementation group I Chain: U
Molecule details ›
Chain: U
Length: 1328 amino acids
Theoretical weight: 149.51 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: B7ZMF2 (Residues: 1-1328; Coverage: 100%)
Gene name: FANCI
Sequence domains:
Fanconi anemia group D2 protein Chain: V
Molecule details ›
Chain: V
Length: 1451 amino acids
Theoretical weight: 164.33 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9BXW9 (Residues: 1-1451; Coverage: 100%)
Gene names: FACD, FANCD2
Sequence domains: Fanconi anaemia protein FancD2 nuclease
Ubiquitin-conjugating enzyme E2 T Chain: X
Molecule details ›
Chain: X
Length: 197 amino acids
Theoretical weight: 22.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NPD8 (Residues: 1-197; Coverage: 100%)
Gene names: HSPC150, PIG50, UBE2T
Sequence domains: Ubiquitin-conjugating enzyme

Ligands and Environments

1 bound ligand:
Ligand ZN 5 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.4Å
Relevant EMDB volumes: EMD-23087
Expression systems:
  • Homo sapiens
  • Spodoptera frugiperda
  • Escherichia coli

Quick links

Citations

8 review citations

DNA repair defects in cancer and therapeutic opportunities.
Hopkins et al. (2022)
7 more

2 mentions without citation

Structure of the FA core ubiquitin ligase closing the ID clamp on DNA.
Wang et al. (2021)
1 more