9gfm

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

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

INO80 complex subunit B

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	Nucleosomal DNA strand 1 × 1 Nucleosomal DNA strand 2 × 1 Histone H3.1 × 1 （P68431） Histone H4 × 1 （P62805） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 2-E × 1 （Q16778） Histone H3.1 × 1 （P68431） Histone H4 × 1 （P62805） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 2-E × 1 （Q16778）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IN80B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 1–50； UniProt 140–189

Histone H3.1

Homo sapiens

UniProt P68431

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	INO80 complex subunit B × 1 （Q9C086） Nucleosomal DNA strand 1 × 1 Nucleosomal DNA strand 2 × 1 Histone H4 × 1 （P62805） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 2-E × 1 （Q16778） Histone H4 × 1 （P62805） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 2-E × 1 （Q16778）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H31_HUMAN
Isoform	—
PDB entities	4, 8
Chains and sequence ranges	Author chain M； PDBConstruct 1–93； UniProt 44–136 Author chain Q； PDBConstruct 1–100； UniProt 37–136

Histone H4

Homo sapiens

UniProt P62805

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	INO80 complex subunit B × 1 （Q9C086） Nucleosomal DNA strand 1 × 1 Nucleosomal DNA strand 2 × 1 Histone H3.1 × 1 （P68431） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 2-E × 1 （Q16778） Histone H3.1 × 1 （P68431） Histone H2A type 1-B/E × 1 （P04908） Histone H2B type 2-E × 1 （Q16778）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_HUMAN
Isoform	—
PDB entities	5, 9
Chains and sequence ranges	Author chain N； PDBConstruct 1–82； UniProt 22–103 Author chain R； PDBConstruct 1–79； UniProt 25–103

Histone H2A type 1-B/E

Homo sapiens

UniProt P04908

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	INO80 complex subunit B × 1 （Q9C086） Nucleosomal DNA strand 1 × 1 Nucleosomal DNA strand 2 × 1 Histone H3.1 × 1 （P68431） Histone H4 × 1 （P62805） Histone H2B type 2-E × 1 （Q16778） Histone H3.1 × 1 （P68431） Histone H4 × 1 （P62805） Histone H2B type 2-E × 1 （Q16778）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1B_HUMAN
Isoform	—
PDB entities	6, 10
Chains and sequence ranges	Author chain O； PDBConstruct 1–106； UniProt 14–119 Author chain S； PDBConstruct 1–111； UniProt 9–119

Histone H2B type 2-E

Homo sapiens

UniProt Q16778

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	INO80 complex subunit B × 1 （Q9C086） Nucleosomal DNA strand 1 × 1 Nucleosomal DNA strand 2 × 1 Histone H3.1 × 1 （P68431） Histone H4 × 1 （P62805） Histone H2A type 1-B/E × 1 （P04908） Histone H3.1 × 1 （P68431） Histone H4 × 1 （P62805） Histone H2A type 1-B/E × 1 （P04908）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B2E_HUMAN
Isoform	—
PDB entities	7, 11
Chains and sequence ranges	Author chain P； PDBConstruct 1–96； UniProt 31–126 Author chain T； PDBConstruct 1–93； UniProt 32–124

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9gfm
Deposition date deposition_date	2024-08-09
Structure title title	CryoEM structure of the human INO80 core-nucleosome complex state N-7
Keywords keywords	Homo sapiens, ATP-dependent chromatin remodeller, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9gfm__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9gfm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9gfm__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	40.98 Å
Rg (electron density)	38.23 Å
Total Rg	38.94 Å
Atom count	12125
Residues	1088
Excluded volume	198000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9gfm__assembly_1__model_1`	11-meric （11）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	INO80 complex subunit B
Molecular weight formula_weight	5759.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	12125

GLGGQEEEEEQRWLDALEKGELDDNGDLKKEINERLLTARQRALLQKARS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Nucleosomal DNA strand 1
Molecular weight formula_weight	43140.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	K

ACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCA

Entity 3 Entity 3 polymer

Description description	Nucleosomal DNA strand 2
Molecular weight formula_weight	42664.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L

TGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGT

Entity 4 Entity 4 polymer

Description description	Histone H3.1
Molecular weight formula_weight	10791.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Histone H4
Molecular weight formula_weight	9279.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Histone H2A type 1-B/E
Molecular weight formula_weight	11637.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

KAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Histone H2B type 2-E
Molecular weight formula_weight	10750.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

KRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 polymer

Description description	Histone H3.1
Molecular weight formula_weight	11762.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

KKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 9 Entity 9 polymer

Description description	Histone H4
Molecular weight formula_weight	8910.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

DNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 10 Entity 10 polymer

Description description	Histone H2A type 1-B/E
Molecular weight formula_weight	12123.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

GKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 11 Entity 11 polymer

Description description	Histone H2B type 2-E
Molecular weight formula_weight	10420.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T

RSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

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Resolution resolution	3.800 Å
Low-resolution limit resolution_low	3.800 Å
R factor r_factor	0.2466
R_work r_work	0.2466
R_free r_free	—

Resolution resolution	3.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	64537

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

INO80 complex subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H3.1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2A type 1-B/E

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2B type 2-E

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9gfm__assembly_1__model_1

9gfm__assembly_1__model_1 | I(q)

9gfm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 polymer

Polymer Polymer

Source Source

Entity 9 Entity 9 polymer

Polymer Polymer

Source Source

Entity 10 Entity 10 polymer

Polymer Polymer

Source Source

Entity 11 Entity 11 polymer