Download MendeleyStructural basis of human CHD1 nucleosome recruitment and pausing
James, A.M., Farnung, L.(2025) Mol Cell
9NH8 | pdb_00009nh8
CHD1-nucleosome complex (anchored state)
- PDB DOI: https://doi.org/10.2210/pdb9NH8/pdb
- EM Map EMD-49406: EMDB EMDataResource
- Classification: nuclear protein/DNA
- Organism(s): Xenopus laevis, synthetic construct, Homo sapiens
- Expression System: Escherichia coli BL21(DE3), synthetic construct, Trichoplusia ni
- Mutation(s): Yes
- Deposited: 2025-02-24 Released: 2025-05-07
- Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.20 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Histone H3.2 | A, E, K [auth V] | 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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Find similar proteins by:
(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 | 130 | Xenopus laevis | Mutation(s): 0 Gene Names: hist1h2aj, LOC494591, XELAEV_18003602mg |  | |
UniProt | |||||
Find proteins for Q6AZJ8 (Xenopus laevis) Explore Q6AZJ8 Go to UniProtKB: Q6AZJ8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6AZJ8 | ||||
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 | 123 | 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: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Chromodomain-helicase-DNA-binding protein 1 | L [auth W] | 1,329 | Homo sapiens | Mutation(s): 0 Gene Names: CHD1 EC: 3.6.4.12 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O14646 (Homo sapiens) Explore O14646 Go to UniProtKB: O14646 | |||||
PHAROS: O14646 GTEx: ENSG00000153922 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O14646 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (158-MER) | 205 | synthetic construct |  | ||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (158-MER) | 205 | synthetic construct |  | ||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ARG Query on ARG | M [auth G] | ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| ML3 Query on ML3 | A, E, K [auth V] | L-PEPTIDE LINKING | C8 H19 N2 O2 S |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.20 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
Entry History & Funding Information
Deposition Data
- Released Date: 2025-05-07 Deposition Author(s): James, A.M., Farnung, L.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Cancer Institute (NIH/NCI) | United States | ES036404 |
Revision History (Full details and data files)
- Version 1.0: 2025-05-07
Type: Initial release
