› 7jzv

Electron Microscopy
3.9Å resolution

Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome

Released:
DOI: 10.2210/pdb7jzv/pdb
PDB entry 7jzv coloured by chain, front view.
PDB entry 7jzv coloured by chain, side view.
PDB entry 7jzv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1.
Witus SR, Burrell AL, Farrell DP, Kang J, Wang M, Hansen JM, Pravat A, Tuttle LM, Stewart MD, Brzovic PS, Chatterjee C, Zhao W, DiMaio F, Kollman JM, Klevit RE
Nat Struct Mol Biol 28 268-277 (2021)
PMID: 33589814
Related structures: EMD-22581

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 dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-121415 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
Breast cancer type 1 susceptibility protein; Ubiquitin-conjugating enzyme E2 D3 Chain: A
Molecule details ›
Chain: A
Length: 258 amino acids
Theoretical weight: 28.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P38398 (Residues: 2-104; Coverage: 6%)
  • Canonical: P61077 (Residues: 2-147; Coverage: 99%)
Gene names: BRCA1, RNF53, UBC5C, UBCH5C, UBE2D3
Sequence domains:
BRCA1-associated RING domain protein 1 Chain: B
Molecule details ›
Chain: B
Length: 115 amino acids
Theoretical weight: 12.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q99728 (Residues: 26-140; Coverage: 15%)
Gene name: BARD1
Sequence domains: zf-RING of BARD1-type protein
Histone H2A type 2-A Chains: N, n
Molecule details ›
Chains: N, n
Length: 133 amino acids
Theoretical weight: 14.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6FI13 (Residues: 2-130; Coverage: 99%)
Gene names: H2AC18, H2AC19, H2AFO, HIST2H2AA, HIST2H2AA3, HIST2H2AA4
Sequence domains:
Histone H2B type 1-K Chains: O, o
Molecule details ›
Chains: O, o
Length: 125 amino acids
Theoretical weight: 13.79 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O60814 (Residues: 2-126; Coverage: 99%)
Gene names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H3.2 Chains: P, p
Molecule details ›
Chains: P, p
Length: 135 amino acids
Theoretical weight: 15.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q71DI3 (Residues: 2-136; Coverage: 99%)
Gene names: H3C13, H3C14, H3C15, H3F2, H3FM, HIST2H3A, HIST2H3C, HIST2H3D
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: Q, q
Molecule details ›
Chains: Q, q
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62805 (Residues: 2-103; Coverage: 99%)
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
Widom 601 153-bp Chain: X
Molecule details ›
Chain: X
Length: 153 nucleotides
Theoretical weight: 47.46 KDa
Widom 601 153-bp Chain: Y
Molecule details ›
Chain: Y
Length: 153 nucleotides
Theoretical weight: 47 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-22581
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 review citations

Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin.
Sanchez et al. (2021)
7 more

8 mentions without citation

Principles of nucleosome recognition by chromatin factors and enzymes.
McGinty et al. (2021)
7 more