ISDA: 8X7K

Deposition Date 2023-11-24

Release Date 2024-08-07

Last Version Date 2025-06-25

Entry Detail

PDB ID:

8X7K

Keywords:

NUCLEAR PROTEIN/DNA

Title:

Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination)

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.27 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 H3.2
Gene (Uniprot):H3C15, H3C14, H3C13
Chain IDs:A, E
Chain Length:97
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q71DI3 Pfam ID:PF00125

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H4
Gene (Uniprot):H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16
Chain IDs:B, F
Chain Length:82
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
Chain Length:105
Number of Molecules:1
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, H
Chain Length:94
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:O60814 Pfam ID:PF00125

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1-B/E
Gene (Uniprot):H2AC4, H2AC8
Chain IDs:G
Chain Length:108
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P04908 Pfam ID:PF00125, PF16211

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (143-MER)
Chain IDs:I
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (143-MER)
Chain IDs:J
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-conjugating enzyme E2 D3
Gene (Uniprot):UBE2D3
Chain IDs:K
Chain Length:147
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61077 Pfam ID:PF00179 EC:2.3.2.23

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin-protein ligase RNF168
Gene (Uniprot):RNF168
Chain IDs:L
Chain Length:113
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8IYW5 Pfam ID:PF14447

Ligand Molecules

Primary Citation

Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168

Ai, H, Tong, Z, Deng, Z, Shi, Q, Tao, S, Liang, J, Sun, M, Wu, X, Zheng, Q, Liang, L, Li, J.B, Gao, S, Tian, C, Liu, L, Pan, M.Show

Biorxiv ? ? ? (2024)

DOI: 10.1101/2024.01.02.573964

Primary Citation of related structures

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