9E1V | pdb_00009e1v

Snf2h bound nucleosome complex - ClassC2

• PDB DOI: https://doi.org/10.2210/pdb9E1V/pdb
• NAKB: 9E1V
• EM Map EMD-47422: 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)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Snf2h bound nucleosome complex-ClassC2

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A6B2C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 325.82 kDa 
• Atom Count: 15,959 
• Modelled Residue Count: 1,513 
• Deposited Residue Count: 2,345 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

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 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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	C, G	130	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897  Go to UniProtKB:  P06897

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 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 ID: 5
Molecule	Chains	Length	Organism	Image
DNA (151-MER)	I	151	Homo sapiens

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (152-MER)	J	152	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	L [auth W]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Malik, D., Deshmukh, A.A., Bilokapic, S., Halic, M.

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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

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release