7JZV: BRCA1-UbcH5c/BARD1 E3-E2 module
Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome. Determined by electron microscopy at 3.9 Å resolution. Released 17 Feb 2021.
- Method
- Electron microscopy
- Resolution
- 3.9 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 12
- Atoms
- 14,339
- Mol. weight
- 245.92 kDa
- Ligands
- ZN
- Released
- 17 Feb 2021
Explore 7JZV in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7JZV contains 51 α-helices and 37 β-strands across 10 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 10 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-21 | 14 | |
| β-strand | 34-36 | 3 | 1 |
| β-strand | 43-44 | 2 | 1 |
| α-helix | 45-52 | 8 | |
| β-strand | 59-60 | 2 | 2 |
| α-helix | 61 | 1 | |
| β-strand | 67-68 | 2 | 2 |
| β-strand | 74-75 | 2 | 1 |
| α-helix | 78-96 | 19 | |
| α-helix | 204-215 | 12 | |
| β-strand | 222-225 | 4 | 3 |
| β-strand | 232-238 | 7 | 3 |
| α-helix | 239-240 | 2 | |
| β-strand | 249-255 | 7 | 3 |
| β-strand | 266 | 1 | 3 |
| β-strand | 268 | 1 | 4 |
| β-strand | 269 | 1 | 3 |
| β-strand | 278 | 1 | 5 |
| β-strand | 283 | 1 | 4 |
| β-strand | 284 | 1 | 5 |
| α-helix | 287-289 | 3 | |
| α-helix | 299-311 | 13 | |
| α-helix | 321-329 | 9 | |
| α-helix | 332-345 | 14 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-45 | 18 | |
| β-strand | 61-63 | 3 | 6 |
| β-strand | 67-70 | 4 | 6 |
| α-helix | 75-80 | 6 | |
| α-helix | 92-94 | 3 | |
| β-strand | 95-97 | 3 | 6 |
| α-helix | 99-121 | 23 | |
Chain n: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 13 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 14 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-97 | 7 | |
| β-strand | 100-102 | 3 | 12 |
| α-helix | 113-115 | 3 | |
Chain N: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 7 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 8 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 9 |
| α-helix | 113-115 | 3 | |
Chain o: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 14 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 13 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-123 | 20 | |
Chain O: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 34-35 | 2 | |
| α-helix | 38-46 | 9 | |
| β-strand | 53-54 | 2 | 8 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 7 |
| α-helix | 91-101 | 11 | |
| α-helix | 106-123 | 18 | |
Chain p: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-55 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 15 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 16 |
| α-helix | 121-132 | 12 | |
Chain P: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-56 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 10 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 11 |
| α-helix | 121-131 | 11 | |
2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| BRCA1,Ubiquitin-conjugating enzyme E2 D3 | A | protein | 258 | Homo sapiens | P38398 (AlphaFold model), P61077 (AlphaFold model) |
| BRCA1-associated RING domain protein 1 | B | protein | 115 | Homo sapiens | Q99728 (AlphaFold model) |
| Histone H2A type 2-A | N, n | protein | 133 | Homo sapiens | Q6FI13 (AlphaFold model) |
| Histone H2B type 1-K | O, o | protein | 125 | Homo sapiens | O60814 |
| Histone H3.2 | P, p | protein | 135 | Homo sapiens | Q71DI3 |
| Histone H4 | Q, q | protein | 102 | Homo sapiens | P62805 |
| Widom 601 153-bp | X | DNA | 153 | synthetic construct | |
| Widom 601 153-bp | Y | DNA | 153 | synthetic construct | |
Sequence of entity 1 (A), FASTA
>7JZV_1 BRCA1,Ubiquitin-conjugating enzyme E2 D3 (chains A)
GPDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPS
QCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSGSGSGSGALKRINKE
LSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAF
TTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKT
DRDKYNRISREWTQKYAM
Sequence of entity 2 (B), FASTA
>7JZV_2 BRCA1-associated RING domain protein 1 (chains B)
MEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPV
CYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLFNDAGNKK
Sequence of entity 3 (N, n), FASTA
>7JZV_3 Histone H2A type 2-A (chains N, n)
GAMGSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLL
PKKTESHHKAKGK
Sequence of entity 4 (O, o), FASTA
>7JZV_4 Histone H2B type 1-K (chains O, o)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK
Sequence of entity 5 (P, p), FASTA
>7JZV_5 Histone H3.2 (chains P, p)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 6 (Q, q), FASTA
>7JZV_6 Histone H4 (chains Q, q)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 7 (X), FASTA
>7JZV_7 Widom 601 153-bp (chains X)
ATCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGT
TAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAA
TTGAGCGGCCTCGGCACCGGGATTCTCCAGGAT
Sequence of entity 8 (Y), FASTA
>7JZV_8 Widom 601 153-bp (chains Y)
ATCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCT
TAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCT
CCAGGCACGTGTCAGATATATACATCCTGTGAT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1. Witus, S.R., Burrell, A.L., Farrell, D.P. et al. Nat Struct Mol Biol (2021) 28:268-277. DOI 10.1038/s41594-020-00556-4 · PubMed
Other PDB entries of the same protein (UniProt P38398 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8RS8 1.31 Å, Crystal structure of BRCA1 BRCTs in complex with a RIF1 phosphopeptide
- 4IGK 1.75 Å, Structure of human BRCA1 BRCT in complex with ATRIP peptide
- 1T15 1.85 Å, Crystal Structure of the Brca1 BRCT Domains in Complex with the Phosphorylated…
- 4IFI 2.2 Å, Structure of human BRCA1 BRCT in complex with BAAT peptide
- 1T29 2.3 Å, Crystal structure of the BRCA1 BRCT repeats bound to a phosphorylated BACH1 peptide
- 1JNX 2.5 Å, Crystal structure of the BRCT repeat region from the breast cancer associated protein,…
- 1Y98 2.5 Å, Structure of the BRCT repeats of BRCA1 bound to a CtIP phosphopeptide.
- 3PXB 2.5 Å, Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: T1700A
- 4Y2G 2.5 Å, Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide
- 3PXA 2.55 Å, Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: G1656D
- 3K0H 2.7 Å, The crystal structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide…
- 3K0K 2.7 Å, Crystal Structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with…
Browse structure collections
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