› 8grq

Electron Microscopy
3.87Å resolution

Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome

Released:
DOI: 10.2210/pdb8grq/pdb
PDB entry 8grq coloured by chain, front view.
PDB entry 8grq coloured by chain, side view.
PDB entry 8grq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Synthetic E2-Ub-nucleosome conjugates for studying nucleosome ubiquitination.
Ai HS, Tong Z, Deng Z, Tian J, Zhang L, Sun M, Du Y, Xu Z, Shi Q, Liang L, Zheng Q, Li JB, Pan M, Liu L
Chem (2023)
Related structures: EMD-34212

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 tridecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-228970 (preferred)
Entry contents:
7 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (9 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 98 amino acids
Theoretical weight: 11.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q71DI3 (Residues: 38-135; Coverage: 72%)
Gene names: H3C13, H3C14, H3C15, H3F2, H3FM, HIST2H3A, HIST2H3C, HIST2H3D
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 80 amino acids
Theoretical weight: 9.12 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62805 (Residues: 23-102; Coverage: 78%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1-B/E Chains: C, G
Molecule details ›
Chains: C, G
Length: 110 amino acids
Theoretical weight: 12.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04908 (Residues: 11-120; Coverage: 85%)
Gene names: H2AC4, H2AC8, H2AFA, H2AFM, HIST1H2AB, HIST1H2AE
Sequence domains:
Histone H2B type 1-K Chains: D, H
Molecule details ›
Chains: D, H
Length: 188 amino acids
Theoretical weight: 20.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60814 (Residues: 32-125; Coverage: 91%)
Gene names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
Sequence domains: Core histone H2A/H2B/H3/H4
Breast cancer type 1 susceptibility protein Chain: K
Molecule details ›
Chain: K
Length: 92 amino acids
Theoretical weight: 10.63 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P38398 (Residues: 6-97; Coverage: 5%)
Gene names: BRCA1, RNF53
Sequence domains: Zinc finger, C3HC4 type (RING finger)
BRCA1-associated RING domain protein 1 Chain: M
Molecule details ›
Chain: M
Length: 92 amino acids
Theoretical weight: 10.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99728 (Residues: 26-117; Coverage: 12%)
Gene name: BARD1
Sequence domains: zf-RING of BARD1-type protein
Ubiquitin-conjugating enzyme E2 D3 Chain: N
Molecule details ›
Chain: N
Length: 147 amino acids
Theoretical weight: 16.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61077 (Residues: 1-147; Coverage: 100%)
Gene names: UBC5C, UBCH5C, UBE2D3
Sequence domains: Ubiquitin-conjugating enzyme
DNA (147-MER) Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.6 KDa
DNA (147-MER) Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.15 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.87Å
Relevant EMDB volumes: EMD-34212
Expression system: Escherichia coli

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