SAXSdb — 9r1d

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

Histone H3 variant

Trypanosoma brucei brucei TREU927

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 （Q587H6） Histone H2A × 2 （Q57YA3） Histone H2B × 2 （Q389T1） Widom 601 145 bp DNA (115-mer ordered and built) × 1 Widom 601 145 bp DNA (115-mer ordered and built) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q387X7_TRYB2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–138； UniProt 2–139 Author chain E； PDBConstruct 1–138； UniProt 2–139

Histone H4

Trypanosoma brucei brucei TREU927

UniProt Q587H6

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 variant × 2 （Q387X7） Histone H2A × 2 （Q57YA3） Histone H2B × 2 （Q389T1） Widom 601 145 bp DNA (115-mer ordered and built) × 1 Widom 601 145 bp DNA (115-mer ordered and built) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q587H6_TRYB2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–99； UniProt 2–100 Author chain F； PDBConstruct 1–99； UniProt 2–100

Histone H2A

Trypanosoma brucei brucei TREU927

UniProt Q57YA3

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 variant × 2 （Q387X7） Histone H4 × 2 （Q587H6） Histone H2B × 2 （Q389T1） Widom 601 145 bp DNA (115-mer ordered and built) × 1 Widom 601 145 bp DNA (115-mer ordered and built) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q57YA3_TRYB2
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–133； UniProt 2–134 Author chain G； PDBConstruct 1–133； UniProt 2–134

Histone H2B

Trypanosoma brucei brucei TREU927

UniProt Q389T1

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 variant × 2 （Q387X7） Histone H4 × 2 （Q587H6） Histone H2A × 2 （Q57YA3） Widom 601 145 bp DNA (115-mer ordered and built) × 1 Widom 601 145 bp DNA (115-mer ordered and built) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q389T1_TRYB2
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–111； UniProt 2–112 Author chain H； PDBConstruct 1–111； UniProt 2–112

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	9r1d
Deposition date deposition_date	2025-04-26
Structure title title	Structure of the H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei
Keywords keywords	nucleosome, histone, nucleus, 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.

9r1d__assembly_1__model_1

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

Download this curve (.dat)

9r1d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9r1d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.23 Å
Rg (electron density)	35.42 Å
Total Rg	36.15 Å
Atom count	9880
Residues	889
Excluded volume	161080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9r1d__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 variant
Molecular weight formula_weight	15920.6 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	9880

AQMKKITPRPVRPKSVASRPIQSVARAPVKKVENTPPQKRHHRWRPGTVALREIRRLQSSTDFLIQRAPFRRFLREVVSNLKDSYRMSAACVDAIQEATETYITSVFMDANLCTLHANRVTLFPKDIQLALKLRGERN

Source Source

Source organism organism	Trypanosoma brucei brucei TREU927
NCBI taxonomy ID ncbi_taxonomy_id	185431
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Histone H4
Molecular weight formula_weight	11150.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AKGKRVGESKGAQKRQKKVLRDNVRGITRGSIRRLARRAGVKRISGVIYDEVRGVLKTFVESIVRDAGAYTEYSRKKTVTAAHVVFALRKRGKVLYGYD

Source Source

Source organism organism	Trypanosoma brucei brucei TREU927
NCBI taxonomy ID ncbi_taxonomy_id	185431
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Histone H2A
Molecular weight formula_weight	14108.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ATPKQAVKKASKGGSSRSVKAGLIFPVGRVGTLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQTKKTKRLTPRTVTLAVRHDDDLGALLRNVTMSRGGVMPSLNKALAKKQKSGKHAKATPSV

Source Source

Source organism organism	Trypanosoma brucei brucei TREU927
NCBI taxonomy ID ncbi_taxonomy_id	185431
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Histone H2B
Molecular weight formula_weight	12464.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ATPKSTPAKTRKEAKKTRRQRKRTWNVYVSRSLRSINSQMSMTSRTMKIVNSFVNDLFERIAAEAATIVRVNRKRTLGARELQTAVRLVLPADLAKHAMAEGTKAVSHASS

Source Source

Source organism organism	Trypanosoma brucei brucei TREU927
NCBI taxonomy ID ncbi_taxonomy_id	185431
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Widom 601 145 bp DNA (115-mer ordered and built)
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	I

ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGAT

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Widom 601 145 bp DNA (115-mer ordered and built)
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	J

ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCGAT

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

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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	3.21 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	362400

Structure of the H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei

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

Histone H3 variant

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

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

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

9r1d__assembly_1__model_1

9r1d__assembly_1__model_1 | I(q)

9r1d__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 (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)