9GCG | pdb_00009gcg

CryoEM structure of the human INO80 core- H2A.Z nucleosome complex

PDB DOI: https://doi.org/10.2210/pdb9GCG/pdb
EM Map EMD-51229: EMDB EMDataResource
NAKB: 9GCG

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

Deposited: 2024-08-01 Released: 2025-08-13
Deposition Author(s): Aggarwal, P., Sharma, M., Hopfner, K.P.
Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.43 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

Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex

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

To be published.

Macromolecule Content

Total Structure Weight: 814.68 kDa
Atom Count: 43,167
Modeled Residue Count: 4,977
Deposited Residue Count: 6,752
Unique protein chains: 11
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like 1	A [auth C], D [auth A], E [auth B]	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	B [auth E], F [auth D], G [auth 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
INO80 complex subunit C	C [auth I]	192	Homo sapiens	Mutation(s): 0 Gene Names: INO80C, C18orf37
UniProt & NIH Common Fund Data Resources
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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin-remodeling ATPase INO80	H [auth G]	1,556	Homo sapiens	Mutation(s): 0 Gene Names: INO80, INO80A, INOC1, KIAA1259 EC: 3.6.4
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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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
INO80 complex subunit B	I [auth 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: 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
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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
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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
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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.Z	O	127	Homo sapiens	Mutation(s): 0 Gene Names: H2AZ1, H2AFZ, H2AZ
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Find proteins for P0C0S5 (Homo sapiens) Explore P0C0S5 Go to UniProtKB: P0C0S5
PHAROS: P0C0S5 GTEx: ENSG00000164032
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0S5
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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: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A.Z	S	127	Homo sapiens	Mutation(s): 0 Gene Names: H2AZ1, H2AFZ, H2AZ
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0S5 (Homo sapiens) Explore P0C0S5 Go to UniProtKB: P0C0S5
PHAROS: P0C0S5 GTEx: ENSG00000164032
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0S5
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Length	Organism	Image
Nucleosomal DNA Strand 1 (152-MER)	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 (152-MER)	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 W [auth A] MOL2 format, chain W [auth A] mmCIF format, chain W [auth A]	W [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain W [auth A] Interactions & Density Focus chain W [auth A]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain CA [auth J] SDF format, chain U [auth C] SDF format, chain V [auth E] SDF format, chain X [auth B] SDF format, chain Y [auth D] SDF format, chain Z [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain CA [auth J] MOL2 format, chain U [auth C] MOL2 format, chain V [auth E] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain CA [auth J] mmCIF format, chain U [auth C] mmCIF format, chain V [auth E] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth F]	AA [auth G] CA [auth J] U [auth C] V [auth E] X [auth B] AA [auth G], CA [auth J], U [auth C], V [auth E], X [auth B], Y [auth D], Z [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth G] Focus chain CA [auth J] Focus chain U [auth C] Focus chain V [auth E] Focus chain X [auth B] Focus chain Y [auth D] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain CA [auth J] Focus chain U [auth C] Focus chain V [auth E] Focus chain X [auth B] Focus chain Y [auth D] 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]