SAXSdb — 1zbb

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

HISTONE H3

Xenopus laevis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 32 DNA 4	DNA STRAND 1 (ARBITRARY MODEL SEQUENCE) × 2 DNA STRAND 2 (ARBITRARY MODEL SEQUENCE) × 2 Histone H4 × 8 （P62799） Histone H2A.1 × 8 （P06897） Histone H2B.1 × 8 （P02281）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H31_XENLA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–135； UniProt 1–135 Author chain E； PDBConstruct 1–135； UniProt 1–135 Author chain a； PDBConstruct 1–135； UniProt 1–135 Author chain e； PDBConstruct 1–135； UniProt 1–135

Histone H4

Xenopus laevis

UniProt P62799

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 32 DNA 4	DNA STRAND 1 (ARBITRARY MODEL SEQUENCE) × 2 DNA STRAND 2 (ARBITRARY MODEL SEQUENCE) × 2 HISTONE H3 × 8 （P84233） Histone H2A.1 × 8 （P06897） Histone H2B.1 × 8 （P02281）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_XENLA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–102； UniProt 1–102 Author chain F； PDBConstruct 1–102； UniProt 1–102 Author chain b； PDBConstruct 1–102； UniProt 1–102 Author chain f； PDBConstruct 1–102； UniProt 1–102

Histone H2A.1

Xenopus laevis

UniProt P06897

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 32 DNA 4	DNA STRAND 1 (ARBITRARY MODEL SEQUENCE) × 2 DNA STRAND 2 (ARBITRARY MODEL SEQUENCE) × 2 HISTONE H3 × 8 （P84233） Histone H4 × 8 （P62799） Histone H2B.1 × 8 （P02281）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1_XENLA
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain C； PDBConstruct 1–129； UniProt 1–129 Author chain G； PDBConstruct 1–129； UniProt 1–129 Author chain c； PDBConstruct 1–129； UniProt 1–129 Author chain g； PDBConstruct 1–129； UniProt 1–129

Histone H2B.1

Xenopus laevis

UniProt P02281

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 32 DNA 4	DNA STRAND 1 (ARBITRARY MODEL SEQUENCE) × 2 DNA STRAND 2 (ARBITRARY MODEL SEQUENCE) × 2 HISTONE H3 × 8 （P84233） Histone H4 × 8 （P62799） Histone H2A.1 × 8 （P06897）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B1_XENLA
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain D； PDBConstruct 1–125； UniProt 1–125 Author chain H； PDBConstruct 1–125； UniProt 1–125 Author chain d； PDBConstruct 1–125； UniProt 1–125 Author chain h； PDBConstruct 1–125； UniProt 1–125

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	1zbb
Deposition date deposition_date	2005-04-08
Structure title title	Structure of the 4_601_167 Tetranucleosome
Keywords keywords	;TETRANUCLEOSOME, NUCLEOSOME, CHROMATIN, CHROMATIN FIBER, HISTONE, PROTEIN-DNA INTERACTION, NUCLEOPROTEIN, SUPERCOILED DNA, NUCLEOSOME CORE, PROTEIN-DNA COMPLEX, STRUCTURAL PROTEIN-DNA COMPLEX ;; STRUCTURAL PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

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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.

1zbb__assembly_1__model_1

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

Download this curve (.dat)

1zbb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zbb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	83.92 Å
Rg (electron density)	84.25 Å
Total Rg	84.24 Å
Atom count	53702
Residues	4564
Excluded volume	868480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zbb__assembly_1__model_1`	36-meric （36）	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	DNA STRAND 1 (ARBITRARY MODEL SEQUENCE)
Molecular weight formula_weight	107153.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I
Atom count atom_count	26851

ACTTACATGCACAGGATGTAACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGATTCTCCAGGGCGGCCAGTACTTACATGCACAGGATGTAACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGATTCTCCAGACTTACATGCGCATGTAAGTGCA

Entity 2 Entity 2 polymer

Description description	DNA STRAND 2 (ARBITRARY MODEL SEQUENCE)
Molecular weight formula_weight	107144.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

TGCACTTACATGCGCATGTAAGTCTGGAGAATCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTTACATCCTGTGCATGTAAGTACTGGCCGCCCTGGAGAATCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTTACATCCTGTGCATGTAAGT

Entity 3 Entity 3 polymer

Description description	HISTONE H3
Molecular weight formula_weight	15303.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Histone H4
Molecular weight formula_weight	11263.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Histone H2A.1
Molecular weight formula_weight	13978.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Histone H2B.1
Molecular weight formula_weight	13848.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1zbba1
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d1zbbb1
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d1zbbd1
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d1zbbe1
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d1zbbf1
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

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Unit-cell length a length_a	127.675 Å
Unit-cell length b length_b	168.445 Å
Unit-cell length c length_c	237.126 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	32

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	9.000 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.3860
R_work r_work	0.3860
R_free r_free	—

Structure of the 4_601_167 Tetranucleosome

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

HISTONE H3

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.1

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.1

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

1zbb__assembly_1__model_1

1zbb__assembly_1__model_1 | I(q)

1zbb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

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

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

7. Citations (1)