SAXSdb — 3c9k

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

Histone H2A-IV

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 704	Histone H2B 7 × 176 （P0C1H5） Histone H3.2 × 176 （P84229） Histone H4 × 176 （P62801）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	Histone H2B 7 × 2 （P0C1H5） Histone H3.2 × 2 （P84229） Histone H4 × 2 （P62801）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 8	Histone H2B 7 × 2 （P0C1H5） Histone H3.2 × 2 （P84229） Histone H4 × 2 （P62801）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A4_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–128； UniProt 2–129 Author chain E； PDBConstruct 1–128； UniProt 2–129

Histone H2B 7

OrganismNot specified

UniProt P0C1H5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 704	Histone H2A-IV × 176 （P02263） Histone H3.2 × 176 （P84229） Histone H4 × 176 （P62801）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	Histone H2A-IV × 2 （P02263） Histone H3.2 × 2 （P84229） Histone H4 × 2 （P62801）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 8	Histone H2A-IV × 2 （P02263） Histone H3.2 × 2 （P84229） Histone H4 × 2 （P62801）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B7_CHICK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–125； UniProt 2–126 Author chain F； PDBConstruct 1–125； UniProt 2–126

Histone H3.2

OrganismNot specified

UniProt P84229

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 704	Histone H2A-IV × 176 （P02263） Histone H2B 7 × 176 （P0C1H5） Histone H4 × 176 （P62801）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	Histone H2A-IV × 2 （P02263） Histone H2B 7 × 2 （P0C1H5） Histone H4 × 2 （P62801）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 8	Histone H2A-IV × 2 （P02263） Histone H2B 7 × 2 （P0C1H5） Histone H4 × 2 （P62801）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H32_CHICK
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–135； UniProt 2–136 Author chain G； PDBConstruct 1–135； UniProt 2–136

Histone H4

OrganismNot specified

UniProt P62801

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 704	Histone H2A-IV × 176 （P02263） Histone H2B 7 × 176 （P0C1H5） Histone H3.2 × 176 （P84229）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	Histone H2A-IV × 2 （P02263） Histone H2B 7 × 2 （P0C1H5） Histone H3.2 × 2 （P84229）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 8	Histone H2A-IV × 2 （P02263） Histone H2B 7 × 2 （P0C1H5） Histone H3.2 × 2 （P84229）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_CHICK
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–102； UniProt 2–103 Author chain H； PDBConstruct 1–102； UniProt 2–103

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	3c9k
Deposition date deposition_date	2008-02-16
Structure title title	Model of Histone Octamer Tubular Crystals
Keywords keywords	helix, tubular crystal, Chromosomal protein, Nucleosome core, Nucleus, Phosphoprotein, Methylation, 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.

3c9k__assembly_1__model_1

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

Download this curve (.dat)

3c9k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c9k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	187.10 Å
Total Rg	187.20 Å
Atom count	501600
Residues	63712
Excluded volume	9009500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c9k__assembly_1__model_1`	704-meric （704）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3c9k__assembly_2__model_1`	octameric （8）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`3c9k__assembly_3__model_1`	octameric （8）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Histone H2A-IV
Molecular weight formula_weight	13838.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	5700

SGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTDSHKAKAK

Entity 2 Entity 2 polymer

Description description	Histone H2B 7
Molecular weight formula_weight	13864.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

PEPAKSAPAPKKGSKKAVTKTQKKGDKKRKRARKESYSIYVYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

Entity 3 Entity 3 polymer

Description description	Histone H3.2
Molecular weight formula_weight	15289.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Entity 4 Entity 4 polymer

Description description	Histone H4
Molecular weight formula_weight	11263.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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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	1

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

Resolution resolution	20.00 Å
Resolution测定Method resolution_method	Iterative Helical Real Space Reconstruction
颗粒数 num_particles	3500

Model of Histone Octamer Tubular Crystals

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

Histone H2A-IV

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2B 7

State in the Current Structure

Other States of the Same Protein in the Database

Histone H3.2

State in the Current Structure

Other States of the Same Protein in the Database

Histone H4

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3c9k__assembly_1__model_1

3c9k__assembly_1__model_1 | I(q)

3c9k__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

7. Citations (1)

Model of Histone Octamer Tubular Crystals

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

Histone H2A-IV

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 7

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 H3.2

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3c9k__assembly_1__model_1

3c9k__assembly_1__model_1 | I(q)

3c9k__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

7. Citations (1)