Download MendeleyStructural visualization of read-write mechanisms of histone H2A lysine 119 mono-ubiquitination by Polycomb Repressive Complex 1
Godinez-Lopez, V., Valencia-Sanchez, M.I., Armache, J.P., Armache, K.-J.To be published.
9DBY
ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
- PDB DOI: https://doi.org/10.2210/pdb9DBY/pdb
- EM Map EMD-46728: EMDB EMDataResource
- Classification: GENE REGULATION/DNA
- Organism(s): Xenopus laevis, synthetic construct, Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2024-08-24 Released: 2024-11-20
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), The Mark Foundation
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 2.80 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
Starting Models: in silico, experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Histone H3.2 | 136 | Xenopus laevis | Mutation(s): 1 |  | |
UniProt | |||||
Find proteins for P84233 (Xenopus laevis) Explore P84233 Go to UniProtKB: P84233 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P84233 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Histone H4 | 103 | Xenopus laevis | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P62799 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Histone H2A type 1 | 130 | Xenopus laevis | Mutation(s): 1 |  | |
UniProt | |||||
Find proteins for P06897 (Xenopus laevis) Explore P06897 Go to UniProtKB: P06897 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06897 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Histone H2B 1.1 | 126 | Xenopus laevis | Mutation(s): 1 |  | |
UniProt | |||||
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P02281 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Histone H2A type 1 | 130 | Xenopus laevis | Mutation(s): 2 |  | |
UniProt | |||||
Find proteins for P06897 (Xenopus laevis) Explore P06897 Go to UniProtKB: P06897 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06897 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 8 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Polycomb complex protein BMI-1 | 326 | Homo sapiens | Mutation(s): 0 Gene Names: BMI1, PCGF4, RNF51 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P35226 (Homo sapiens) Explore P35226 Go to UniProtKB: P35226 | |||||
PHAROS: P35226 GTEx: ENSG00000168283 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P35226 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 9 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| E3 ubiquitin-protein ligase RING2 | 336 | Homo sapiens | Mutation(s): 0 Gene Names: RNF2, BAP1, DING, HIPI3, RING1B EC: 2.3.2.27 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q99496 (Homo sapiens) Explore Q99496 Go to UniProtKB: Q99496 | |||||
PHAROS: Q99496 GTEx: ENSG00000121481 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q99496 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 10 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| RING1 and YY1-binding protein | 228 | Homo sapiens | Mutation(s): 0 Gene Names: RYBP, DEDAF, YEAF1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q8N488 (Homo sapiens) Explore Q8N488 Go to UniProtKB: Q8N488 | |||||
PHAROS: Q8N488 GTEx: ENSG00000163602 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8N488 | ||||
Sequence AnnotationsExpand | |||||
| |||||
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(by identity cutoff) | 3D Structure
Entity ID: 11 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ubiquitin | 76 | Homo sapiens | Mutation(s): 1 Gene Names: UBB |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47 | |||||
PHAROS: P0CG47 GTEx: ENSG00000170315 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0CG47 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (187-MER) | 187 | synthetic construct |  | ||
Sequence AnnotationsExpand | |||||
| |||||
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(by identity cutoff) | 3D Structure
Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (187-MER) | 187 | synthetic construct |  | ||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | O [auth K], P [auth K], Q [auth L], R [auth L], S [auth M] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 2.80 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| MODEL REFINEMENT | PHENIX | 1.20.1 |
| RECONSTRUCTION | cryoSPARC | 4.4 |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-11-20 Deposition Author(s): Godinez-Lopez, V., Valencia-Sanchez, M.I., Armache, J.P., Armache, K.-J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R01GM115882 |
| National Institutes of Health/National Cancer Institute (NIH/NCI) | United States | R01CA266978 |
| The Mark Foundation | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2024-11-20
Type: Initial release
