SAXSdb — 7xd0

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

Histone H4

Homo sapiens

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 H2A × 2 （Q08AJ9） Histone H2B type 1-K × 2 （Q2M2T1） Histone domain-containing protein × 2 （S4RAZ3） DNA (146-MER) × 1 DNA (146-MER) × 1 Ubiquitin-60S ribosomal protein L40 × 2 （A0A2H6N1E9）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A672PXK1_SINGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–83； UniProt 12–94 Author chain F； PDBConstruct 1–83； UniProt 12–94

Histone H2A

Homo sapiens

UniProt Q08AJ9

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 （A0A672PXK1） Histone H2B type 1-K × 2 （Q2M2T1） Histone domain-containing protein × 2 （S4RAZ3） DNA (146-MER) × 1 DNA (146-MER) × 1 Ubiquitin-60S ribosomal protein L40 × 2 （A0A2H6N1E9）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q08AJ9_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–108； UniProt 12–119 Author chain G； PDBConstruct 1–108； UniProt 12–119

Histone H2B type 1-K

OrganismNot specified

UniProt Q2M2T1

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 （A0A672PXK1） Histone H2A × 2 （Q08AJ9） Histone domain-containing protein × 2 （S4RAZ3） DNA (146-MER) × 1 DNA (146-MER) × 1 Ubiquitin-60S ribosomal protein L40 × 2 （A0A2H6N1E9）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B1K_BOVIN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–92； UniProt 34–125 Author chain H； PDBConstruct 1–92； UniProt 34–125

Histone domain-containing protein

Homo sapiens

UniProt S4RAZ3

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 （A0A672PXK1） Histone H2A × 2 （Q08AJ9） Histone H2B type 1-K × 2 （Q2M2T1） DNA (146-MER) × 1 DNA (146-MER) × 1 Ubiquitin-60S ribosomal protein L40 × 2 （A0A2H6N1E9）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	S4RAZ3_PETMA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 61–159 Author chain E； PDBConstruct 1–99； UniProt 61–159

Ubiquitin-60S ribosomal protein L40

OrganismNot specified

UniProt A0A2H6N1E9

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 （A0A672PXK1） Histone H2A × 2 （Q08AJ9） Histone H2B type 1-K × 2 （Q2M2T1） Histone domain-containing protein × 2 （S4RAZ3） DNA (146-MER) × 1 DNA (146-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2H6N1E9_MICLE
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain K； PDBConstruct 1–76； UniProt 1–76 Author chain L； PDBConstruct 1–76； UniProt 1–76

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	7xd0
Deposition date deposition_date	2022-03-26
Structure title title	cryo-EM structure of H2BK34ub nucleosome
Keywords keywords	H2BK34ub nucleosome, NUCLEAR PROTEIN; NUCLEAR 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.

7xd0__assembly_1__model_1

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

Download this curve (.dat)

7xd0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7xd0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.96 Å
Rg (electron density)	40.15 Å
Total Rg	40.70 Å
Atom count	13222
Residues	1207
Excluded volume	216890 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7xd0__assembly_1__model_1`	dodecameric （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 (7)

Entity 1 Entity 1 polymer

Description description	Histone H4
Molecular weight formula_weight	9409.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,B
Atom count atom_count	13222

KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Histone H2A
Molecular weight formula_weight	11865.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

RAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Histone H2B type 1-K
Molecular weight formula_weight	10233.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

RKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA

Entity 4 Entity 4 polymer

Description description	Histone domain-containing protein
Molecular weight formula_weight	11631.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	DNA (146-MER)
Molecular weight formula_weight	44825.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGAT

Entity 6 Entity 6 polymer

Description description	DNA (146-MER)
Molecular weight formula_weight	45305.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGA

Entity 7 Entity 7 polymer

Description description	Ubiquitin-60S ribosomal protein L40
Molecular weight formula_weight	8576.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,K

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	7xd0A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	7xd0B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	7xd0C01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	7xd0D01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	7xd0E01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	7xd0G01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	7xd0H01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	7xd0K01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	7xd0L01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 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	3.48 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	85558

cryo-EM structure of H2BK34ub nucleosome

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

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 1-K

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 domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-60S ribosomal protein L40

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

7xd0__assembly_1__model_1

7xd0__assembly_1__model_1 | I(q)

7xd0__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 (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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)