9ECP | pdb_00009ecp

Structure of the native human NCP purified from HEK293 cells

• PDB DOI: https://doi.org/10.2210/pdb9ECP/pdb
• EM Map EMD-47924: EMDB EMDataResource
• NAKB: 9ECP

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


• Deposited: 2024-11-14 Released: 2025-10-22 
• Deposition Author(s): Reid, X.J., Sobti, M., Low, J.K.K., Stewart, A.G., Mackay, J.P.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 1.91 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The structure and composition of native human nucleosomes

Reid, X.J., Sobti, M., Zeng, Y.C., Zhong, Y., Deshpande, C., Young, P., Brown, S.H.J., Low, J.K.K., Stewart, A.G., Mackay, J.P.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.10.10.681767

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: Hetero 8-mer - A6B2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 175.42 kDa 
• Atom Count: 12,239 
• Modeled Residue Count: 1,052 
• Deposited Residue Count: 1,052 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E	96	Homo sapiens	Mutation(s): 0  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	82	Homo sapiens	Mutation(s): 0  Gene Names:  H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 3	C, G	109	Homo sapiens	Mutation(s): 0  Gene Names: H2AC25, H2AW, HIST3H2A
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L7L0 (Homo sapiens) Explore Q7L7L0  Go to UniProtKB:  Q7L7L0
PHAROS:  Q7L7L0 GTEx:  ENSG00000181218

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-K	D, H	94	Homo sapiens	Mutation(s): 0  Gene Names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens) Explore O60814  Go to UniProtKB:  O60814
PHAROS:  O60814 GTEx:  ENSG00000197903

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (145-MER)	I, J	145	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 1.91 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: 2025-10-22 
Deposition Author(s): Reid, X.J., Sobti, M., Low, J.K.K., Stewart, A.G., Mackay, J.P.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release