SAXSdb — 8com

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

Histone H3, putative

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 （Q57Z31） Histone H2A × 2 （Q57YA3） Histone H2B × 2 （Q389T1） Widom 601 145 bp DNA (127-mer ordered and built) × 1 Widom 601 145 bp DNA (127-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	Q4GYX7_TRYB2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–132； UniProt 2–133 Author chain E； PDBConstruct 1–132； UniProt 2–133

Histone H4

Trypanosoma brucei brucei TREU927

UniProt Q57Z31

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, putative × 2 （Q4GYX7） Histone H2A × 2 （Q57YA3） Histone H2B × 2 （Q389T1） Widom 601 145 bp DNA (127-mer ordered and built) × 1 Widom 601 145 bp DNA (127-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	Q57Z31_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, putative × 2 （Q4GYX7） Histone H4 × 2 （Q57Z31） Histone H2B × 2 （Q389T1） Widom 601 145 bp DNA (127-mer ordered and built) × 1 Widom 601 145 bp DNA (127-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, putative × 2 （Q4GYX7） Histone H4 × 2 （Q57Z31） Histone H2A × 2 （Q57YA3） Widom 601 145 bp DNA (127-mer ordered and built) × 1 Widom 601 145 bp DNA (127-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	8com
Deposition date deposition_date	2023-02-28
Structure title title	Structure of the Nucleosome Core Particle from Trypanosoma brucei
Keywords keywords	Nucleosome Chromatin Parasite Trypanosome Kinetoplast, 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.

8com__assembly_1__model_1

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

Download this curve (.dat)

8com__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8com__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)	35.51 Å
Total Rg	36.23 Å
Atom count	10705
Residues	962
Excluded volume	173990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8com__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, putative
Molecular weight formula_weight	14647.9 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	10705

SRTKETARTKKTITSKKSKKASKGSDAASGVKTAQRRWRPGTVALREIRQFQRSTDLLLQKAPFQRLVREVSGAQKEGLRFQSSAILAAQEATESYIVSLLADTNRACIHSGRVTIQPKDIHLALCLRGERA

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	11037.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AKGKKSGEAKGSQKRQKKVLRENVRGITRGSIRRLARRGGVKRISGVIYDEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAVDVVNALRKRGKILYGYA

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 (127-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 K2

Entity 6 Entity 6 polymer

Description description	Widom 601 145 bp DNA (127-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 K2

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Resolution resolution	3.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	306475

Structure of the Nucleosome Core Particle from Trypanosoma brucei

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

Histone H3, putative

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

8com__assembly_1__model_1

8com__assembly_1__model_1 | I(q)

8com__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)