9nh8

CHD1-nucleosome complex (anchored state)

Method: ELECTRON MICROSCOPY

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

Histone H3.2

Xenopus laevis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 2	Histone H4 × 2 （P62799） Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） DNA (158-MER) × 1 DNA (158-MER) × 1 Chromodomain-helicase-DNA-binding protein 1 × 1 （O14646） ARGININE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H32_XENLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 1–136 Author chain E； PDBConstruct 1–136； UniProt 1–136 Author chain V； PDBConstruct 1–136； UniProt 1–136

Histone H4

Xenopus laevis

UniProt P62799

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 2	Histone H3.2 × 3 （P84233） Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） DNA (158-MER) × 1 DNA (158-MER) × 1 Chromodomain-helicase-DNA-binding protein 1 × 1 （O14646） ARGININE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_XENLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–103； UniProt 1–103 Author chain F； PDBConstruct 1–103； UniProt 1–103

Histone H2A

Xenopus laevis

UniProt Q6AZJ8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 2	Histone H3.2 × 3 （P84233） Histone H4 × 2 （P62799） Histone H2B 1.1 × 2 （P02281） DNA (158-MER) × 1 DNA (158-MER) × 1 Chromodomain-helicase-DNA-binding protein 1 × 1 （O14646） ARGININE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6AZJ8_XENLA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–130； UniProt 1–130 Author chain G； PDBConstruct 1–130； UniProt 1–130

Histone H2B 1.1

Xenopus laevis

UniProt P02281

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 2	Histone H3.2 × 3 （P84233） Histone H4 × 2 （P62799） Histone H2A × 2 （Q6AZJ8） DNA (158-MER) × 1 DNA (158-MER) × 1 Chromodomain-helicase-DNA-binding protein 1 × 1 （O14646） ARGININE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B11_XENLA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 2–123； UniProt 5–126 Author chain H； PDBConstruct 2–123； UniProt 5–126

Chromodomain-helicase-DNA-binding protein 1

Homo sapiens

UniProt O14646

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 2	Histone H3.2 × 3 （P84233） Histone H4 × 2 （P62799） Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） DNA (158-MER) × 1 DNA (158-MER) × 1 ARGININE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CHD1_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain W； PDBConstruct 4–1329； UniProt 2–1327

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	9nh8
Deposition date deposition_date	2025-02-24
Structure title title	CHD1-nucleosome complex (anchored state)
Keywords keywords	chromatin, remodeler, genome organization, nuclear protein, nuclear protein-DNA complex; nuclear protein/DNA
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.

9nh8__assembly_1__model_1

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

Download this curve (.dat)

9nh8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9nh8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.05 Å
Rg (electron density)	45.81 Å
Total Rg	46.16 Å
Atom count	18500
Residues	1803
Excluded volume	309140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9nh8__assembly_1__model_1`	12-meric （12）	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 (8)

Entity 1 Entity 1 polymer

Description description	Histone H3.2
Molecular weight formula_weight	15463.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,V
Atom count atom_count	18500

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Histone H4
Molecular weight formula_weight	11394.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Histone H2A
Molecular weight formula_weight	14109.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Histone H2B 1.1
Molecular weight formula_weight	13655.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H

MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	DNA (158-MER)
Molecular weight formula_weight	63146.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

AACTAAAGCTTAGATGTGCGAATTCCAGCCATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCGATAGGCACTGATTGATTACTAGGAATAACAGG

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	synthetic construct

Entity 6 Entity 6 polymer

Description description	DNA (158-MER)
Molecular weight formula_weight	63434.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

CCTGTTATTCCTAGTAATCAATCAGTGCCTATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGATGGCTGGAATTCGCACATCTAAGCTTTAGTT

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	synthetic construct

Entity 7 Entity 7 polymer

Description description	Chromodomain-helicase-DNA-binding protein 1
Molecular weight formula_weight	151787.7 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W

SNANGHSDEESVRNSSGESSQSDDDSGSASGSGSGSSSGSSSDGSSSQSGSSDSDSGSESGSQSESESDTSRENKVQAKPPKVDGAEFWKSSPSILAVQRSAILKKQQQQQQQQQHQASSNSGSEEDSSSSEDSDDSSSEVKRKKHKDEDWQMSGSGSPSQSGSDSESEEEREKSSCDETESDYEPKNKVKSRKPQNRSKSKNGKKILGQKKRQIDSSEEDDDEEDYDNDKRSSRRQATVNVSYKEDEEMKTDSDDLLEVCGEDVPQPEEEEFETIERFMDCRIGRKGATGATTTIYAVEADGDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQELTDDLHKQYQIVERIIAHSNQKSAAGYPDYYCKWQGLPYSECSWEDGALISKKFQACIDEYFSRNQSKTTPFKDCKVLKQRPRFVALKKQPSYIGGHEGLELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLTSWQREIQTWASQMNAVVYLGDINSRNMIRTHEWTHHQTKRLKFNILLTTYEILLKDKAFLGGLNWAFIGVDEAHRLKNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGKGREYGYASLHKELEPFLLRRVKKDVEKSLPAKVEQILRMEMSALQKQYYKWILTRNYKALSKGSKGSTSGFLNIMMELKKCCNHCYLIKPPDNNEFYNKQEALQHLIRSSGKLILLDKLLIRLRERGNRVLIFSQMVRMLDILAEYLKYRQFPFQRLDGSIKGELRKQALDHFNAEGSEDFCFLLSTRAGGLGINLASADTVVIFDSDWNPQNDLQAQARAHRIGQKKQVNIYRLVTKGSVEEDILERAKKKMVLDHLVIQRMDTTGKTVLHTGSAPSSSTPFNKEELSAILKFGAEELFKEPEGEEQEPQEMDIDEILKRAETHENEPGPLTVGDELLSQFKVANFSNMDEDDIELEPERNSKNWEEIIPEDQRRRLEEEERQKELEEIYMLPRMRNCAKQISFNGSEGRRSRSRRYSGSDSDSISEGKRPKKRGRPRTIPRENIKGFSDAEIRRFIKSYKKFGGPLERLDAIARDAELVDKSETDLRRLGELVHNGCIKALKDSSSGTERTGGRLGKVKGPTFRISGVQVNAKLVISHEEELIPLHKSIPSDPEERKQYTIPCHTKAAHFDIDWGKEDDSNLLIGIYEYGYGSWEMIKMDPDLSLTHKILPDDPDKKPQAKQLQTRADYLIKLLSRDLAKKEALSGAG

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 8 Entity 8 non-polymer

Description description	ARGININE
Molecular weight formula_weight	175.2 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	67512

CHD1-nucleosome complex (anchored state)

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

Histone H3.2

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

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 1.1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Chromodomain-helicase-DNA-binding protein 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9nh8__assembly_1__model_1

9nh8__assembly_1__model_1 | I(q)

9nh8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

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 non-polymer

7. Citations (1)