7LYB: Human nucleosome core particle
Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c. Determined by electron microscopy at 3.28 Å resolution. Released 28 Jul 2021.
- Method
- Electron microscopy
- Resolution
- 3.28 Å
- Organism
- Homo sapiens
- Chains
- 13
- Atoms
- 14,699
- Mol. weight
- 241.83 kDa
- Ligands
- ZN
- Released
- 28 Jul 2021
Explore 7LYB in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7LYB contains 53 α-helices and 35 β-strands across 11 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.
Chains A and E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-131 | 11 | |
Chains B and F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 3 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 28-35 | 8 | |
| β-strand | 42-43 | 2 | 5 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 4 |
| α-helix | 80-89 | 10 | |
| α-helix | 92-96 | 5 | |
| β-strand | 101-102 | 2 | 8 |
| α-helix | 113-115 | 3 | |
Chain D: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-33 | 3 | |
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 4 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 5 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-122 | 19 | |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 28-36 | 9 | |
| β-strand | 42-43 | 2 | 10 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 9 |
| α-helix | 80-89 | 10 | |
| α-helix | 92-96 | 5 | |
| β-strand | 101-102 | 2 | 3 |
| α-helix | 113-115 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 9 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 10 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-122 | 19 | |
Chain M: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-21 | 14 | |
| β-strand | 23 | 1 | 11 |
| β-strand | 30 | 1 | 11 |
| β-strand | 35-36 | 2 | 12 |
| β-strand | 43 | 1 | 12 |
| α-helix | 49-52 | 4 | |
| β-strand | 59-60 | 2 | 13 |
| β-strand | 66-68 | 3 | 13 |
| β-strand | 74-75 | 2 | 12 |
| α-helix | 80-96 | 17 | |
Chain N: 5 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 49 | 1 | 15 |
| β-strand | 56 | 1 | 15 |
| β-strand | 60-61 | 2 | 16 |
| β-strand | 70-71 | 2 | 16 |
| α-helix | 72-75 | 4 | |
| α-helix | 88-90 | 3 | |
| α-helix | 96-98 | 3 | |
| α-helix | 99-115 | 17 | |
1 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 |
|---|
| Histone H3.1 | A, E | protein | 140 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 107 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2B type 1-J | D, H | protein | 126 | Homo sapiens | P06899 (AlphaFold model) |
| DNA (147-mer) | I | DNA | 147 | Homo sapiens | |
| DNA (146-mer) | J | DNA | 147 | Homo sapiens | |
| Isoform 7 of Breast cancer type 1 susceptibility protein | M | protein | 124 | Homo sapiens | P38398 (AlphaFold model) |
| Ubiquitin-conjugating enzyme E2 D3 | P | protein | 165 | Homo sapiens | P61077 |
| BRCA1-associated RING domain protein 1 | N | protein | 97 | Homo sapiens | Q99728 |
| Histone H2A type 1-B/E | C, G | protein | 119 | Homo sapiens | P04908 |
Sequence of entity 1 (A, E), FASTA
>7LYB_1 Histone H3.1 (chains A, E)
GPGHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQ
KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAK
RVTIMPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>7LYB_2 Histone H4 (chains B, F)
GPGHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETR
GVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (D, H), FASTA
>7LYB_3 Histone H2B type 1-J (chains D, H)
GHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSK
AMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKA
VTKYTS
Sequence of entity 4 (I), FASTA
>7LYB_4 DNA (147-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT
Sequence of entity 5 (J), FASTA
>7LYB_5 DNA (146-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT
Sequence of entity 6 (M), FASTA
>7LYB_6 Isoform 7 of Breast cancer type 1 susceptibility protein (chains M)
GGSGGSGGSGGSGGSGGSGGSGGSMDLSALRVEEVQNVINAMQKILECPICLELIKEPVS
TKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLD
TGLE
Sequence of entity 7 (P), FASTA
>7LYB_7 Ubiquitin-conjugating enzyme E2 D3 (chains P)
GGSGGSGGSGGSGGSGGSSALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPND
SPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKV
LLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM
Sequence of entity 8 (N), FASTA
>7LYB_8 BRCA1-associated RING domain protein 1 (chains N)
MEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPV
CYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSD
Sequence of entity 9 (C, G), FASTA
>7LYB_9 Histone H2A type 1-B/E (chains C, G)
SAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAA
RDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation. Hu, Q., Botuyan, M.V., Zhao, D. et al. Nature (2021) 596:438-443. DOI 10.1038/s41586-021-03716-8 · PubMed
Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
- 2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
- 5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
- 5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
- 5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
- 4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
- 6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail
Browse structure collections
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