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
• EM Map EMD-44470: EMDB EMDataResource
• NAKB: 9BE5

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-14 Released: 2025-04-30 
• Deposition Author(s): Jia, L., Ruben, E.A., Olsen, S.K., Wasmuth, E.V.
• 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: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 8-mer - A8 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 175.27 kDa 
• Atom Count: 11,898 
• Modeled Residue Count: 1,041 
• Deposited Residue Count: 1,049 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A	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 GTEx:  ENSG00000183598 ENSG00000203811 ENSG00000203852

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	83	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for A0A9J8D176 (Cyprinus carpio carpio) Explore A0A9J8D176  Go to UniProtKB:  A0A9J8D176

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	C	103	Homo sapiens	Mutation(s): 0  Gene Names:  H2AC11, H2AFP, HIST1H2AG, H2AC13, H2AFC, HIST1H2AI, H2AC15, H2AFD, HIST1H2AK, H2AC16, H2AFI, HIST1H2AL, H2AC17, H2AFN, HIST1H2AM
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0S8 (Homo sapiens) Explore P0C0S8  Go to UniProtKB:  P0C0S8
PHAROS:  P0C0S8 GTEx:  ENSG00000196747 ENSG00000196787 ENSG00000278677 ENSG00000276903

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	D, H	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 ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	E	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 GTEx:  ENSG00000183598 ENSG00000203811 ENSG00000203852

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	G	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 GTEx:  ENSG00000277075 ENSG00000278463

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (145-MER)	I	145	Homo sapiens

Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (145-MER)	J	145	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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.

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

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release
  
• Version 1.1: 2025-05-21
  Changes: Data collection