9GF6 | pdb_00009gf6

CryoEM structure of the human INO80 core-nucleosome complex state N-6

• PDB DOI: https://doi.org/10.2210/pdb9GF6/pdb
• NAKB: 9GF6
• EM Map EMD-51310: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2024-08-08 Released: 2025-08-20 
• Deposition Author(s): Sharma, M., Aggarwal, P., Hopfner, K.P.
• Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

CryoEM structure of the human INO80 core-nucleosome complex state N-6

Sharma, M., Aggarwal, P., Hopfner, K.P.

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 - A7B1C1 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: 241.65 kDa 
• Atom Count: 11,865 
• Modeled Residue Count: 1,068 
• Deposited Residue Count: 1,644 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	C [auth M], G [auth Q]	136	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	D [auth N], H [auth R]	102	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, 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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	E [auth O], I [auth S]	129	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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 2-E	F [auth P], J [auth T]	125	Homo sapiens	Mutation(s): 0  Gene Names: H2BC21, H2BFQ, HIST2H2BE
UniProt & NIH Common Fund Data Resources
Find proteins for Q16778 (Homo sapiens) Explore Q16778  Go to UniProtKB:  Q16778
PHAROS:  Q16778 GTEx:  ENSG00000184678

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
INO80 complex subunit B	K [auth H]	356	Homo sapiens	Mutation(s): 0  Gene Names: INO80B, HMGA1L4, PAPA1, ZNHIT4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C086 (Homo sapiens) Explore Q9C086  Go to UniProtKB:  Q9C086
GTEx:  ENSG00000115274

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Nucleosomal DNA Strand 1	A [auth K]	152	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Nucleosomal DNA Strand 2	B [auth L]	152	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	REFMAC	5.8.0425

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Sharma, M., Aggarwal, P., Hopfner, K.P.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	833613 INO3D
German Research Foundation (DFG)	Germany	HO 2489/9-1

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release