SAXSdb — 9d3p

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

Histone H3.2

Homo sapiens

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 H4 × 2 （P62805） Histone H2A type 2-A × 2 （Q6FI13） Histone H2B type 1-M × 2 （Q99879） 5S rDNA (noncoding strand) × 1 5S rDNA (coding strand) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H32_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 38–136 Author chain E； PDBConstruct 1–99； UniProt 38–136

Histone H4

Homo sapiens

UniProt P62805

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 H3.2 × 2 （Q71DI3） Histone H2A type 2-A × 2 （Q6FI13） Histone H2B type 1-M × 2 （Q99879） 5S rDNA (noncoding strand) × 1 5S rDNA (coding strand) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–82； UniProt 22–103 Author chain F； PDBConstruct 1–82； UniProt 22–103

Histone H2A type 2-A

Homo sapiens

UniProt Q6FI13

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 H3.2 × 2 （Q71DI3） Histone H4 × 2 （P62805） Histone H2B type 1-M × 2 （Q99879） 5S rDNA (noncoding strand) × 1 5S rDNA (coding strand) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A2A_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–107； UniProt 13–119 Author chain G； PDBConstruct 1–107； UniProt 13–119

Histone H2B type 1-M

Homo sapiens

UniProt Q99879

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 H3.2 × 2 （Q71DI3） Histone H4 × 2 （P62805） Histone H2A type 2-A × 2 （Q6FI13） 5S rDNA (noncoding strand) × 1 5S rDNA (coding strand) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B1M_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–95； UniProt 32–126 Author chain H； PDBConstruct 1–95； UniProt 32–126

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	9d3p
Deposition date deposition_date	2024-08-11
Structure title title	167-bp 5S rDNA nucleosome - open I (open only on the downstream side)
Keywords keywords	;5S rDNA nucleosome, natural nucleosome positioning sequence, DNA sequence-dependent breathing, GENE REGULATION, GENE REGULATION-DNA complex ;; GENE REGULATION/DNA
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.

9d3p__assembly_1__model_1

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

Download this curve (.dat)

9d3p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9d3p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.77 Å
Rg (electron density)	36.07 Å
Total Rg	36.80 Å
Atom count	11063
Residues	1008
Excluded volume	181230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9d3p__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 H3.2
Molecular weight formula_weight	11617.6 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	11063

KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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

Entity 2 Entity 2 polymer

Description description	Histone H4
Molecular weight formula_weight	9279.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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

Entity 3 Entity 3 polymer

Description description	Histone H2A type 2-A
Molecular weight formula_weight	11668.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPK

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

Entity 4 Entity 4 polymer

Description description	Histone H2B type 1-M
Molecular weight formula_weight	10623.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

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

Entity 5 Entity 5 polymer

Description description	5S rDNA (noncoding strand)
Molecular weight formula_weight	38058.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

CTTGTTTTCCTGCCTGGGGGAAAAGACCCTGGCATGGGGAGGAGCTGGGCCCCCCCCAGAAGGCAGCACAAGGGGAGGAAAAGTCAGCCTTGTGCTCGCCTACGGCCATACCACCCTGAAAGT

Source Source

Source organism organism	Xenopus borealis
Common name common_name	Kenyan clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8354
Host organism host_organism	synthetic construct

Entity 6 Entity 6 polymer

Description description	5S rDNA (coding strand)
Molecular weight formula_weight	37866.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

ACTTTCAGGGTGGTATGGCCGTAGGCGAGCACAAGGCTGACTTTTCCTCCCCTTGTGCTGCCTTCTGGGGGGGGCCCAGCTCCTCCCCATGCCAGGGTCTTTTCCCCCAGGCAGGAAAACAAG

Source Source

Source organism organism	Xenopus borealis
Common name common_name	Kenyan clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8354
Host organism host_organism	synthetic construct

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

Resolution resolution	2.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	280478

167-bp 5S rDNA nucleosome - open I (open only on the downstream side)

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

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

Histone H2A type 2-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

Histone H2B type 1-M

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

9d3p__assembly_1__model_1

9d3p__assembly_1__model_1 | I(q)

9d3p__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

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)