SAXSdb — 7vbm

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

Histone H4

Mus musculus

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 H3mm18 × 2 Histone H2A type 1-B × 2 （C0HKE1） Histone H2B type 3-A × 2 （Q9D2U9） DNA (126-MER) × 1 DNA (126-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–106； UniProt 1–103 Author chain F； PDBConstruct 4–106； UniProt 1–103

Histone H2A type 1-B

Mus musculus

UniProt C0HKE1

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 H3mm18 × 2 Histone H4 × 2 （P62806） Histone H2B type 3-A × 2 （Q9D2U9） DNA (126-MER) × 1 DNA (126-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1B_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–133； UniProt 1–130 Author chain G； PDBConstruct 4–133； UniProt 1–130

Histone H2B type 3-A

Mus musculus

UniProt Q9D2U9

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 H3mm18 × 2 Histone H4 × 2 （P62806） Histone H2A type 1-B × 2 （C0HKE1） DNA (126-MER) × 1 DNA (126-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B3A_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 4–129； UniProt 1–126 Author chain H； PDBConstruct 4–129； UniProt 1–126

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	7vbm
Deposition date deposition_date	2021-08-31
Structure title title	The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv
Keywords keywords	complex, chromatin, nucleosome, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; 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.

7vbm__assembly_1__model_1

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

Download this curve (.dat)

7vbm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7vbm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.27 Å
Rg (electron density)	36.46 Å
Total Rg	37.19 Å
Atom count	10475
Residues	929
Excluded volume	170360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7vbm__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 H3mm18
Molecular weight formula_weight	15350.8 kDa
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	10475

GSHMARTKQTARKSTGDKAPRKQLATKAARKSAPSTGGVKKPHCYRPGTVALREIRSYQKSSELLIRKLPFQRLVLEIAQDFKTDLCFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDTQLAGYICRECA

Source Source

Source organism organism	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone H4
Molecular weight formula_weight	11676.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Histone H2A type 1-B
Molecular weight formula_weight	14447.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Histone H2B type 3-A
Molecular weight formula_weight	14307.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSHMPEPSRSTPAPKKGSKKAITKAQKKDGKKRKRGRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIASEASRLAHYNKRSTITSREVQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	DNA (126-MER)
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	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	DNA (126-MER)
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	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

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Resolution resolution	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	224465

The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv

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

Histone H4

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2A type 1-B

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2B type 3-A

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

7vbm__assembly_1__model_1

7vbm__assembly_1__model_1 | I(q)

7vbm__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 (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)

The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv

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

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

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 3-A

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

7vbm__assembly_1__model_1

7vbm__assembly_1__model_1 | I(q)

7vbm__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 (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)