ISDA

Deposition Date 2023-11-24

Release Date 2024-08-07

Last Version Date 2024-08-07

Entry Detail

PDB ID:

8X7I

Keywords:

NUCLEAR PROTEIN/DNA

Title:

Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.27 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Gene (Uniprot):H3C15, H3C14, H3C13
Chain IDs:A, D (auth: E)
Chain Length:98
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q71DI3 Pfam ID:PF00125

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, E (auth: F)
Chain Length:83
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P62805 Pfam ID:PF15511

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1-B/E
Gene (Uniprot):H2AC4, H2AC8
Chain IDs:C
Chain Length:111
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P04908 Pfam ID:PF00125, PF16211

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2B type 1-K
Gene (Uniprot):H2BC12
Chain IDs:I (auth: D), J (auth: H)
Chain Length:94
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:O60814 Pfam ID:PF00125

Protein Blast

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

UniProt ID:P04908 Pfam ID:PF00125, PF16211

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (147-MER)
Chain IDs:G (auth: I)
Chain Length:147
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (147-MER)
Chain IDs:H (auth: J)
Chain Length:147
Number of Molecules:1
Biological Source:Homo sapiens

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

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin
Gene (Uniprot):RPS27A
Chain IDs:M
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62979 Pfam ID:PF00240

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