9E1X | pdb_00009e1x

Snf2h bound nucleosome complex - ClassD1

PDB DOI: https://doi.org/10.2210/pdb9E1X/pdb
NAKB: 9E1X
EM Map EMD-47424: EMDB EMDataResource

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Xenopus laevis, Homo sapiens
Expression System: Escherichia coli, synthetic construct
Mutation(s): Yes

Deposited: 2024-10-21 Released: 2025-01-22
Deposition Author(s): Malik, D., Deshmukh, A.A., Bilokapic, S., Halic, M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Mechanisms of chromatin remodeling by the human Snf2-type ATPase SNF2H.

Malik, D., Deshmukh, A., Bilokapic, S., Halic, M.

(2025) Cell Res 35: 465-468

PubMed: 40175616 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-025-01103-w
Primary Citation of Related Structures:
9E1L, 9E1M, 9E1N, 9E1O, 9E1P, 9E1Q, 9E1R, 9E1U, 9E1V, 9E1W, 9E1X

Organizational Affiliation

Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.

Macromolecule Content

Total Structure Weight: 325.86 kDa
Atom Count: 15,885
Modeled Residue Count: 1,510
Deposited Residue Count: 2,345
Unique protein chains: 5
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	136	Xenopus laevis	Mutation(s): 0
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 Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	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 Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	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 Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	D, H	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 Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5	K [auth W]	1,052	Homo sapiens	Mutation(s): 0 Gene Names: SMARCA5 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for O60264 (Homo sapiens) Explore O60264 Go to UniProtKB: O60264
PHAROS: O60264 GTEx: ENSG00000153147
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60264
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (149-MER)	I	151	Homo sapiens
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (150-MER)	J	152	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain L [auth W] MOL2 format, chain L [auth W] mmCIF format, chain L [auth W]	L [auth W]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain L [auth W] Interactions & Density Focus chain L [auth W]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM135599
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM141694