Download MendeleySynthetic 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.(2023) Chem
8GRQ | pdb_00008grq
Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome
- PDB DOI: https://doi.org/10.2210/pdb8GRQ/pdb
- NAKB: 8GRQ
- EM Map EMD-34212: EMDB EMDataResource
- Classification: NUCLEAR PROTEIN
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2022-09-02 Released: 2023-04-12
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.87 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
Macromolecules
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(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Histone H3 | 98 | Homo sapiens | Mutation(s): 0 Gene Names: CALMAC_LOCUS17614 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q71DI3 (Homo sapiens) Explore Q71DI3 Go to UniProtKB: Q71DI3 | |||||
PHAROS: Q71DI3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q71DI3 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Histone H4 | 80 | Homo sapiens | Mutation(s): 0 Gene Names: Dana\GF27365, Dana_GF27365, GF27365 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P62805 (Homo sapiens) Explore P62805 Go to UniProtKB: P62805 | |||||
PHAROS: P62805 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P62805 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Histone H2A type 1-H | 110 | Homo sapiens | Mutation(s): 0 Gene Names: H2ac12, Hist1h2ah |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P04908 (Homo sapiens) Explore P04908 Go to UniProtKB: P04908 | |||||
PHAROS: P04908 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P04908 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| H2B | 188 | Homo sapiens | Mutation(s): 0 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O60814 (Homo sapiens) Explore O60814 Go to UniProtKB: O60814 | |||||
PHAROS: O60814 GTEx: ENSG00000197903 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O60814 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Breast cancer type 1 susceptibility protein | 92 | Homo sapiens | Mutation(s): 0 Gene Names: BRCA1, RNF53 EC: 2.3.2.27 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P38398 (Homo sapiens) Explore P38398 Go to UniProtKB: P38398 | |||||
PHAROS: P38398 GTEx: ENSG00000012048 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P38398 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 8 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| BRCA1-associated RING domain protein 1 | L [auth M] | 92 | Homo sapiens | Mutation(s): 0 Gene Names: BARD1 EC: 2.3.2.27 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q99728 (Homo sapiens) Explore Q99728 Go to UniProtKB: Q99728 | |||||
PHAROS: Q99728 GTEx: ENSG00000138376 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q99728 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 9 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a | M [auth N] | 147 | Homo sapiens | Mutation(s): 0 Gene Names: UBE2D3, hCG_2028213 EC: 2.3.2.24 (UniProt), 2.3.2.23 (UniProt) |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P61077 (Homo sapiens) Explore P61077 Go to UniProtKB: P61077 | |||||
PHAROS: P61077 GTEx: ENSG00000109332 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P61077 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN (Subject of Investigation/LOI) Query on ZN | N [auth K], O [auth K], P [auth M], Q [auth M] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.87 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
Entry History & Funding Information
Deposition Data
- Released Date: 2023-04-12 Deposition Author(s): Ai, H.S., Zebin, T., Zhiheng, D., Jiakun, T., Liying, Z., Jia-Bin, L., Man, P., Liu, L.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China (NSFC) | China | 22137005, 81621002 and 21977090 |
Revision History (Full details and data files)
- Version 1.0: 2023-04-12
Type: Initial release - Version 1.1: 2024-07-03
Changes: Data collection
