SAXSdb — 9qik

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

Histone H2A type 1

Xenopus laevis laevis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	Histone H2B 1.1 × 2 （P02281） Histone H3 × 2 （A0A8T2P505） Histone H4 × 2 （A0A8J1LTD2） DNA (220-MER) × 1 DNA (220-MER) × 1	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–130； UniProt 1–130 Author chain B； PDBConstruct 1–130； UniProt 1–130

Histone H2B 1.1

Xenopus laevis 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 8 DNA 2	Histone H2A type 1 × 2 （P06897） Histone H3 × 2 （A0A8T2P505） Histone H4 × 2 （A0A8J1LTD2） DNA (220-MER) × 1 DNA (220-MER) × 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	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–126； UniProt 1–126 Author chain D； PDBConstruct 1–126； UniProt 1–126

Histone H3

Xenopus laevis

UniProt A0A8T2P505

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） Histone H4 × 2 （A0A8J1LTD2） DNA (220-MER) × 1 DNA (220-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8T2P505_9TELE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–136； UniProt 1–136 Author chain F； PDBConstruct 1–136； UniProt 1–136

Histone H4

Xenopus laevis laevis

UniProt A0A8J1LTD2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） Histone H3 × 2 （A0A8T2P505） DNA (220-MER) × 1 DNA (220-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8J1LTD2_XENLA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain G； PDBConstruct 1–103； UniProt 14–116 Author chain H； PDBConstruct 1–103； UniProt 14–116

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	9qik
Deposition date deposition_date	2025-03-17
Structure title title	M2 nucleosome
Keywords keywords	NCP, chromatin remodeling, TRANSLOCASE; TRANSLOCASE
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.

9qik__assembly_1__model_1

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

Download this curve (.dat)

9qik__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qik__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.09 Å
Rg (electron density)	36.32 Å
Total Rg	37.07 Å
Atom count	10927
Residues	966
Excluded volume	177590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qik__assembly_1__model_1`	decameric （10）	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 (6)

Entity 1 Entity 1 polymer

Description description	Histone H2A type 1
Molecular weight formula_weight	13993.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	10927

MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKKTESAKSAKSK

Source Source

Source organism organism	Xenopus laevis laevis
NCBI taxonomy ID ncbi_taxonomy_id	443947
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone H2B 1.1
Molecular weight formula_weight	13965.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source Source

Source organism organism	Xenopus laevis laevis
NCBI taxonomy ID ncbi_taxonomy_id	443947
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Histone H3
Molecular weight formula_weight	15361.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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 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	G,H

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Xenopus laevis laevis
NCBI taxonomy ID ncbi_taxonomy_id	443947
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	DNA (220-MER)
Molecular weight formula_weight	68160.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

TTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAATTCGAGCTCGGTACTCGGGTTCAATACATGCATGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTTGCTACTAGTCTCCAGGCACGTGTCAGATATATACATCCTGGGGCG

Source Source

Source organism organism	Xenopus laevis laevis
NCBI taxonomy ID ncbi_taxonomy_id	443947
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	DNA (220-MER)
Molecular weight formula_weight	67698.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

CGCCCCAGGATGTATATATCTGACACGTGCCTGGAGACTAGTAGCAAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCATGCATGTATTGAACCCGAGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAA

Source Source

Source organism organism	Xenopus laevis laevis
NCBI taxonomy ID ncbi_taxonomy_id	443947
Host organism host_organism	Escherichia coli

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Resolution resolution	3.030 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.03 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	93970

M2 nucleosome

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9qik__assembly_1__model_1

9qik__assembly_1__model_1 | I(q)

9qik__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 (6)

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

7. Citations (1)