9GFB | pdb_00009gfb

CryoEM structure of the human INO80 core-nucleosome complex state N-7

PDB DOI: https://doi.org/10.2210/pdb9GFB/pdb
EM Map EMD-51312: EMDB EMDataResource
NAKB: 9GFB

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Trichoplusia ni, Escherichia coli
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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.55 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

CryoEM structure of the human INO80 core-nucleosome complex state N-7

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

To be published.

Macromolecule Content

Total Structure Weight: 815.42 kDa
Atom Count: 43,132
Modeled Residue Count: 5,013
Deposited Residue Count: 6,756
Unique protein chains: 10
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like 1	A, B, C	456	Homo sapiens	Mutation(s): 0 Gene Names: RUVBL1, INO80H, NMP238, TIP49, TIP49A EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y265 (Homo sapiens) Explore Q9Y265 Go to UniProtKB: Q9Y265
PHAROS: Q9Y265 GTEx: ENSG00000175792
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y265
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like 2	D, E, F	463	Homo sapiens	Mutation(s): 0 Gene Names: RUVBL2, INO80J, TIP48, TIP49B, CGI-46 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y230 (Homo sapiens) Explore Q9Y230 Go to UniProtKB: Q9Y230
PHAROS: Q9Y230 GTEx: ENSG00000183207
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y230
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin-remodeling ATPase INO80	G	1,556	Homo sapiens	Mutation(s): 0 Gene Names: INO80, INO80A, INOC1, KIAA1259 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULG1 (Homo sapiens) Explore Q9ULG1 Go to UniProtKB: Q9ULG1
PHAROS: Q9ULG1 GTEx: ENSG00000128908
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9ULG1
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
INO80 complex subunit B	H	356	Homo sapiens	Mutation(s): 0 Gene Names: INO80B, HMGA1L4, PAPA1, ZNHIT4
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Find proteins for Q9C086 (Homo sapiens) Explore Q9C086 Go to UniProtKB: Q9C086
GTEx: ENSG00000115274
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9C086
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
INO80 complex subunit C	I	192	Homo sapiens	Mutation(s): 0 Gene Names: INO80C, C18orf37
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Find proteins for Q6PI98 (Homo sapiens) Explore Q6PI98 Go to UniProtKB: Q6PI98
PHAROS: Q6PI98 GTEx: ENSG00000153391
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6PI98
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 5	J	607	Homo sapiens	Mutation(s): 0 Gene Names: ACTR5, ARP5
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Find proteins for Q9H9F9 (Homo sapiens) Explore Q9H9F9 Go to UniProtKB: Q9H9F9
PHAROS: Q9H9F9 GTEx: ENSG00000101442
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H9F9
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	M, Q	136	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD... 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68431
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	N, R	102	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D... 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62805
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	O, S	129	Homo sapiens	Mutation(s): 0 Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
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Find proteins for P04908 (Homo sapiens) Explore P04908 Go to UniProtKB: P04908
PHAROS: P04908 GTEx: ENSG00000277075 ENSG00000278463
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04908
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 2-E	P, T	125	Homo sapiens	Mutation(s): 0 Gene Names: H2BC21, H2BFQ, HIST2H2BE
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Find proteins for Q16778 (Homo sapiens) Explore Q16778 Go to UniProtKB: Q16778
PHAROS: Q16778 GTEx: ENSG00000184678
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16778
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Length	Organism	Image
Nucleosomal DNA strand 1	K	152	synthetic construct
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Length	Organism	Image
Nucleosomal DNA strand 2	L	152	synthetic construct
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A] mmCIF format, chain U [auth A]	U [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain V [auth B] SDF format, chain W [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain V [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain V [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth F]	AA [auth G] V [auth B] W [auth C] X [auth D] Y [auth E] AA [auth G], V [auth B], W [auth C], X [auth D], Y [auth E], Z [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth G] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth H] MOL2 format, chain BA [auth H] mmCIF format, chain BA [auth H]	BA [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Interactions & Density Focus chain BA [auth H]