Download MendeleyCryo-EM structure of Human Nucleosome collected by EPU on Glacios at 3.3 Angstrom resolution
Jia, L., Ruben, E.A., Olsen, S.K., Wasmuth, E.V.To be published.
9BE5 | pdb_00009be5
Cryo-EM structure of Human Nucleosome collected by EPU on Glacios at 3.3 Angstrom resolution
- PDB DOI: https://doi.org/10.2210/pdb9BE5/pdb
- NAKB: 9BE5
- EM Map EMD-44470: EMDB EMDataResource
- Classification: DNA BINDING PROTEIN/DNA
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2024-04-14 Released: 2025-04-30
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.30 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
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 | 97 | Homo sapiens | Mutation(s): 0 Gene Names: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D |  | |
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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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Histone H4 | 83 | Homo sapiens | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for A0A9J8D176 (Cyprinus carpio carpio) Explore A0A9J8D176 Go to UniProtKB: A0A9J8D176 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A9J8D176 | ||||
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 | 103 | Homo sapiens | Mutation(s): 0 Gene Names: |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P0C0S8 (Homo sapiens) Explore P0C0S8 Go to UniProtKB: P0C0S8 | |||||
PHAROS: P0C0S8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0C0S8 | ||||
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 type 1-J | 95 | Homo sapiens | Mutation(s): 0 Gene Names: H2BC11, H2BFR, HIST1H2BJ |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P06899 (Homo sapiens) Explore P06899 Go to UniProtKB: P06899 | |||||
PHAROS: P06899 GTEx: ENSG00000124635 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06899 | ||||
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 H3.2 | 98 | Homo sapiens | Mutation(s): 0 Gene Names: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D |  | |
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 | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Histone H2A type 1-B/E | 105 | Homo sapiens | Mutation(s): 0 Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE |  | |
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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Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (145-MER) | 145 | Homo sapiens |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 8 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (145-MER) | 145 | Homo sapiens |  | ||
Sequence AnnotationsExpand | |||||
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Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.30 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| MODEL REFINEMENT | PHENIX | |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-04-30 Deposition Author(s): Jia, L., Ruben, E.A., Olsen, S.K., Wasmuth, E.V.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2025-04-30
Type: Initial release - Version 1.1: 2025-05-21
Changes: Data collection
