6zhy

Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: hexasome class.

Method: ELECTRON MICROSCOPY

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

Histone H3

Xenopus laevis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	Histone H4 × 2 （P62799） Histone H2A type 1 × 1 （P06897） Histone H2B 1.1 × 1 （P02281） DNA (110-MER) Widom 601 sequence × 1 DNA (110-MER) Widom 601 sequence × 1 Chromodomain-helicase-DNA-binding protein 1-like × 1 （Q86WJ1）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A310TTQ1_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

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 7 DNA 2	Histone H3 × 2 （A0A310TTQ1） Histone H2A type 1 × 1 （P06897） Histone H2B 1.1 × 1 （P02281） DNA (110-MER) Widom 601 sequence × 1 DNA (110-MER) Widom 601 sequence × 1 Chromodomain-helicase-DNA-binding protein 1-like × 1 （Q86WJ1）	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 type 1

Xenopus laevis

UniProt P06897

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Histone H2B 1.1 × 1 （P02281） DNA (110-MER) Widom 601 sequence × 1 DNA (110-MER) Widom 601 sequence × 1 Chromodomain-helicase-DNA-binding protein 1-like × 1 （Q86WJ1）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1_XENLA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； 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 7 DNA 2	Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Histone H2A type 1 × 1 （P06897） DNA (110-MER) Widom 601 sequence × 1 DNA (110-MER) Widom 601 sequence × 1 Chromodomain-helicase-DNA-binding protein 1-like × 1 （Q86WJ1）	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

Chromodomain-helicase-DNA-binding protein 1-like

OrganismNot specified

UniProt Q86WJ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Histone H2A type 1 × 1 （P06897） Histone H2B 1.1 × 1 （P02281） DNA (110-MER) Widom 601 sequence × 1 DNA (110-MER) Widom 601 sequence × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CHD1L_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain K； PDBConstruct 1–36； UniProt 604–639

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	6zhy
Deposition date deposition_date	2020-06-24
Structure title title	Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: hexasome class.
Keywords keywords	ALC1, CHD1L, chromatin remodeler, DNA damage response, nucleosome, hexasome, NUCLEAR PROTEIN, GENE REGULATION, 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.

6zhy__assembly_1__model_1

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

Download this curve (.dat)

6zhy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6zhy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.44 Å
Rg (electron density)	35.86 Å
Total Rg	36.56 Å
Atom count	8999
Residues	782
Excluded volume	146110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6zhy__assembly_1__model_1`	nonameric （9）	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 (7)

Entity 1 Entity 1 polymer

Description description	Histone H3
Molecular weight formula_weight	15403.1 kDa
Mutation mutation	C110A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	8999

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

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

Entity 3 Entity 3 polymer

Description description	Histone H2A type 1
Molecular weight formula_weight	14109.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

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

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

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

Entity 5 Entity 5 polymer

Description description	DNA (110-MER) Widom 601 sequence
Molecular weight formula_weight	44520.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCGAT

Source Source

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

Entity 6 Entity 6 polymer

Description description	DNA (110-MER) Widom 601 sequence
Molecular weight formula_weight	44991.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGAT

Source Source

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

Entity 7 Entity 7 polymer

Description description	Chromodomain-helicase-DNA-binding protein 1-like
Molecular weight formula_weight	4073.7 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

EKASQEGRSLRNKGSVLIPGLVEGSTKRKRVLSPEEK

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Resolution resolution	3.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	414641

Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: hexasome class.

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

Histone H3

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

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-like

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

6zhy__assembly_1__model_1

6zhy__assembly_1__model_1 | I(q)

6zhy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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

7. Citations (5)