ISDA: 8GRM

Deposition Date 2022-09-02

Release Date 2023-04-12

Last Version Date 2025-06-25

Entry Detail

PDB ID:

8GRM

Keywords:

NUCLEAR PROTEIN

Title:

Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.05 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H3
Chain IDs:A, E
Chain Length:98
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P68431 Pfam ID:PF00125

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:B, F
Chain Length:85
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P62805 Pfam ID:PF15511

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1-B/E
Gene (Uniprot):H2AC4, H2AC8
Chain IDs:C, G
Chain Length:109
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P04908 Pfam ID:PF00125, PF16211

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2B type 1-K
Gene (Uniprot):H2BC12
Chain IDs:D
Chain Length:96
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O60814 Pfam ID:PF00125

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2B type 1-K
Gene (Uniprot):H2BC12
Chain IDs:H
Chain Length:95
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O60814 Pfam ID:PF00125

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (144-MER)
Chain IDs:K (auth: I)
Chain Length:144
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (145-MER)
Chain IDs:L (auth: J)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:COMMD3 protein
Chain IDs:I (auth: M)
Chain Length:101
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P35226 Pfam ID:PF13923

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ring1B
Gene (Uniprot):RNF2
Chain IDs:J (auth: N)
Chain Length:101
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q99496 Pfam ID:PF13923 EC:2.3.2.27

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin
Gene (Uniprot):UBB
Chain IDs:M (auth: O)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P0CG47 Pfam ID:PF00240

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:UbcH5b
Chain IDs:N (auth: P)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62837 Pfam ID:PF00179

Ligand Molecules

Primary Citation

Synthetic E2-Ub-nucleosome conjugates for studying nucleosome ubiquitination.

Ai, H.S, Tong, Z, Deng, Z, Tian, J, Zhang, L, Sun, M, Du, Y, Xu, Z, Shi, Q, Liang, L, Zheng, Q, Li, J.B, Pan, M, Liu, L.Show

Chem ? ? ? (2023)

DOI: 10.1016/j.chempr.2023.01.012

Primary Citation of related structures

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