8GRM: PRC1
Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome. Determined by electron microscopy at 3.05 Å resolution. Released 12 Apr 2023.
- Method
- Electron microscopy
- Resolution
- 3.05 Å
- Organism
- Homo sapiens
- Chains
- 14
- Atoms
- 15,415
- Mol. weight
- 225.89 kDa
- Ligands
- ZN
- Released
- 12 Apr 2023
Explore 8GRM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8GRM contains 55 α-helices and 50 β-strands across 12 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: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-74 | 11 | |
| α-helix | 75-77 | 3 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-130 | 10 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 3 |
Chains C and G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-87 | 8 | |
| α-helix | 93-96 | 4 | |
| β-strand | 100-102 | 3 | 6 |
| α-helix | 117-118 | 2 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 5 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 4 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-118 | 14 | |
Chain E: 7 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 65-74 | 10 | |
| α-helix | 75-77 | 3 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 120 | 1 | |
| α-helix | 121-130 | 10 | |
Chain F: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 50-73 | 24 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-91 | 9 | |
| β-strand | 96-98 | 3 | 6 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 10 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 9 |
| α-helix | 92-101 | 10 | |
| α-helix | 105-121 | 17 | |
Chain M: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-8 | 2 | 11 |
| β-strand | 17 | 1 | 12 |
| β-strand | 24 | 1 | 12 |
| β-strand | 28-31 | 4 | 13 |
| β-strand | 37-39 | 3 | 13 |
| α-helix | 40-46 | 7 | |
| β-strand | 52 | 1 | 14 |
| β-strand | 59 | 1 | 14 |
| β-strand | 69-71 | 3 | 13 |
| α-helix | 73-82 | 10 | |
| α-helix | 87-98 | 12 | |
3 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 | A, E | protein | 98 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 85 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | C, G | protein | 109 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-K | D | protein | 96 | Homo sapiens | O60814 (AlphaFold model) |
| Histone H2B type 1-K | H | protein | 95 | Homo sapiens | O60814 (AlphaFold model) |
| COMMD3 protein | M | protein | 101 | Homo sapiens | P35226 |
| Ring1B | N | protein | 101 | Homo sapiens | Q99496 |
| DNA (144-mer) | I | DNA | 144 | Homo sapiens | |
| DNA (145-mer) | J | DNA | 145 | Homo sapiens | |
| Ubiquitin | O | protein | 76 | Homo sapiens | P0CG47 |
| UbcH5b | P | protein | 146 | Homo sapiens | P62837 |
Sequence of entity 1 (A, E), FASTA
>8GRM_1 Histone H3 (chains A, E)
KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEAC
EAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER
Sequence of entity 2 (B, F), FASTA
>8GRM_2 Histone H4 (chains B, F)
HRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAK
RKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>8GRM_3 Histone H2A type 1-B/E (chains C, G)
RAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAA
RDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
Sequence of entity 4 (D), FASTA
>8GRM_4 Histone H2B type 1-K (chains D)
KRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTI
TSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
Sequence of entity 5 (H), FASTA
>8GRM_5 Histone H2B type 1-K (chains H)
RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
Sequence of entity 6 (M), FASTA
>8GRM_6 COMMD3 protein (chains M)
HRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVH
KTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHP
Sequence of entity 7 (N), FASTA
>8GRM_7 Ring1B (chains N)
TWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADC
LITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPS
Sequence of entity 8 (I), FASTA
>8GRM_8 DNA (144-MER) (chains I)
CGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAAC
GCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGG
CACGTGTCAGATATATACATCCGA
Sequence of entity 9 (J), FASTA
>8GRM_9 DNA (145-MER) (chains J)
TCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTCGA
Sequence of entity 10 (O), FASTA
>8GRM_10 Ubiquitin (chains O)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Sequence of entity 11 (P), FASTA
>8GRM_11 UbcH5b (chains P)
ALKRIHKELNDLARDPPAQSSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYP
FKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSISSLLSDPNPDDPLVP
EIARIYKTDREKYNRIAREWTQKYAM
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
Synthetic E2-Ub-nucleosome conjugates for studying nucleosome ubiquitination. Ai, H.S., Tong, Z., Deng, Z. et al. Chem (2023). DOI 10.1016/j.chempr.2023.01.012
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
About this viewer
MolViewer shows 8GRM directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.