ISDA: 9V9Y

Deposition Date 2025-06-02

Release Date 2026-06-10

Last Version Date 2026-06-10

Entry Detail

PDB ID:

9V9Y

Keywords:

GENE REGULATION

Title:

Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ub-modified nucleosome

Biological Source:

Source Organism(s):

Xenopus laevis (Taxon ID: 8355)
Homo sapiens (Taxon ID: 9606)

Expression System(s):

Escherichia coli, Homo sapiens

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.20 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
Gene (Uniprot):LOC121398065
Chain IDs:A, E
Chain Length:136
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:A0A310TTQ1 Pfam ID:PF00125

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:B, F
Chain Length:103
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:P62799 Pfam ID:PF15511

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2A
Gene (Uniprot):LOC494591
Mutagens:K119C
Chain IDs:C, G
Chain Length:130
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:Q6AZJ8 Pfam ID:PF00125, PF16211

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2B
Gene (Uniprot):LOC108704304
Chain IDs:D, H
Chain Length:126
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:A0A8J0TWI5 Pfam ID:PF00125

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (131-MER)
Chain IDs:I
Chain Length:131
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (132-MER)
Chain IDs:J
Chain Length:132
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin
Gene (Uniprot):UBB
Mutagens:G76C
Chain IDs:M (auth: K)
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:RING1 and YY1-binding protein
Gene (Uniprot):RYBP
Chain IDs:N (auth: L)
Chain Length:228
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8N488 Pfam ID:PF00641, PF17219

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Polycomb complex protein BMI-
Gene (Uniprot):BMI1
Chain IDs:K (auth: M)
Chain Length:326
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P35226 Pfam ID:PF13923, PF16207

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin-protein ligase R
Gene (Uniprot):RNF2
Chain IDs:L (auth: N)
Chain Length:336
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q99496 Pfam ID:PF13923, PF16207 EC:2.3.2.27

Ligand Molecules

Primary Citation

Structural mechanisms of PRC1-mediated interplay between gene repression and activation

Yu, Y, Cai, D, Zhang, Y.Z, Huang, J.Show

To Be Published ? ? ? (?)

Primary Citation of related structures

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