9W6T | pdb_00009w6t

Cryo-EM structure of a stacked human nucleosome core particle dimer (type 5) assembled with DNA truncated at SHL-5.5

• PDB DOI: https://doi.org/10.2210/pdb9W6T/pdb
• NAKB: 9W6T
• EM Map EMD-65703: EMDB EMDataResource

• Classification: GENE REGULATION/DNA
• Organism(s): Homo sapiens, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-08-05 Released: 2026-08-12 
• Deposition Author(s): Mu, Z., Huang, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.61 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for nucleosome stacking diversity mediated by solvent-exposed histone interfaces

Mu, Z., Huang, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 16-mer - A4B4C4D4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 16-mer - A16 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - B4D4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2C2 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: 324.75 kDa 
• Atom Count: 21,588 
• Modeled Residue Count: 1,910 
• Deposited Residue Count: 1,986 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E, K, O	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
GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F, L, P	84	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
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 1-D	C, G, M, Q	102	Homo sapiens	Mutation(s): 0  Gene Names: H2AC7, H2AFG, HIST1H2AD
UniProt & NIH Common Fund Data Resources
Find proteins for P20671 (Homo sapiens) Explore P20671  Go to UniProtKB:  P20671
GTEx:  ENSG00000196866

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-B	D, H, N	87	Homo sapiens	Mutation(s): 0  Gene Names: H2BC3, H2BFF, HIST1H2BB
UniProt & NIH Common Fund Data Resources
Find proteins for P33778 (Homo sapiens) Explore P33778  Go to UniProtKB:  P33778
GTEx:  ENSG00000276410

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	R	85	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
GTEx:  ENSG00000124635

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (128-MER)	I, S	128	Escherichia coli

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (128-MER)	J, T	128	Escherichia coli

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.61 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	RELION

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-12 
Deposition Author(s): Mu, Z., Huang, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-08-12
  Type: Initial release