5wcu

Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5

Method: X-RAY DIFFRACTION

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

Histone H3

Drosophila melanogaster

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） DNA (167-MER) × 1 DNA (167-MER) × 1 Histone H5 × 1 （P02259）	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） DNA (167-MER) × 1 DNA (167-MER) × 1 Histone H5 × 1 （P02259）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H3_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–98； UniProt 39–136 Author chain E； PDBConstruct 1–98； UniProt 39–136 Author chain K； PDBConstruct 1–98； UniProt 39–136 Author chain O； PDBConstruct 1–98； UniProt 39–136

Histone H4

Drosophila melanogaster

UniProt P84040

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H3 × 2 （P02299） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） DNA (167-MER) × 1 DNA (167-MER) × 1 Histone H5 × 1 （P02259）	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H3 × 2 （P02299） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） DNA (167-MER) × 1 DNA (167-MER) × 1 Histone H5 × 1 （P02259）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_DROME
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 Author chain L； PDBConstruct 1–82； UniProt 22–103 Author chain P； PDBConstruct 1–82； UniProt 22–103

Histone H2A

Drosophila melanogaster

UniProt P84051

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2B × 2 （P02283） DNA (167-MER) × 1 DNA (167-MER) × 1 Histone H5 × 1 （P02259）	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2B × 2 （P02283） DNA (167-MER) × 1 DNA (167-MER) × 1 Histone H5 × 1 （P02259）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A_DROME
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–104； UniProt 15–118 Author chain G； PDBConstruct 1–104； UniProt 15–118 Author chain M； PDBConstruct 1–104； UniProt 15–118 Author chain Q； PDBConstruct 1–104； UniProt 15–118

Histone H2B

Drosophila melanogaster

UniProt P02283

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） DNA (167-MER) × 1 DNA (167-MER) × 1 Histone H5 × 1 （P02259）	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） DNA (167-MER) × 1 DNA (167-MER) × 1 Histone H5 × 1 （P02259）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B_DROME
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–94； UniProt 29–122 Author chain H； PDBConstruct 1–94； UniProt 29–122 Author chain N； PDBConstruct 1–94； UniProt 29–122 Author chain R； PDBConstruct 1–94； UniProt 29–122

Histone H5

Gallus gallus

UniProt P02259

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） DNA (167-MER) × 1 DNA (167-MER) × 1	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） DNA (167-MER) × 1 DNA (167-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H5_CHICK
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain U； PDBConstruct 1–76； UniProt 23–98 Author chain V； PDBConstruct 1–76； UniProt 23–98

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	5wcu
Deposition date deposition_date	2017-07-02
Structure title title	Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5
Keywords keywords	;NUCLEOSOME CORE PARTICLE, HISTONE FOLD, CHROMOSOME, CHROMATIN, GLOBULAR DOMAIN, HISTONE H5, GH5, 167 BP NUCLEOSOME, CHROMATOSOME, NUCLEOSOME PACKING, 30 NM CHROMATIN FIBER, LINKER HISTONE H5, LINKER DNA, NUCLEOSOME BINDING PROTEIN, PROTEIN DNA COMPLEXES, DNA BINDING, CHROMATIN HIGHER ORDER STRUCTURE, CHROMATIN FOLDING, CHROMATIN BINDING PROTEIN-DNA complex ;; CHROMATIN BINDING 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.

5wcu__assembly_1__model_1

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

Download this curve (.dat)

5wcu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5wcu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.89 Å
Rg (electron density)	40.45 Å
Total Rg	41.06 Å
Atom count	13301
Residues	1158
Excluded volume	215400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5wcu__assembly_1__model_1`	undecameric （11）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5wcu__assembly_2__model_1`	undecameric （11）	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 H3
Molecular weight formula_weight	11488.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,K,O
Atom count atom_count	26619

PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
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	4

Polymer Polymer

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

VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Histone H2A
Molecular weight formula_weight	11352.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

KSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPK

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Histone H2B
Molecular weight formula_weight	10592.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

RKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	DNA (167-MER)
Molecular weight formula_weight	51318.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,S

ATCGGCCGCCATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGATGCATGTAGAT

Entity 6 Entity 6 polymer

Description description	DNA (167-MER)
Molecular weight formula_weight	51790.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J,T

ATCTACATGCATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGATGGCGGCCGAT

Entity 7 Entity 7 polymer

Description description	Histone H5
Molecular weight formula_weight	8199.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,V

SASHPTYSEMIAAAIRAEKSRGGSSRQSIQKYIKSHYKVGHNADLQIKLSIRRLLAAGVLKQTKGVGASGSFRLAK

Source Source

Source organism organism	Gallus gallus
Common name common_name	Chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	65.926 Å
Unit-cell length b length_b	108.543 Å
Unit-cell length c length_c	180.770 Å
Unit-cell angle α angle_alpha	100.79 °
Unit-cell angle β angle_beta	90.08 °
Unit-cell angle γ angle_gamma	89.94 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	5.530 Å
Low-resolution limit resolution_low	48.620 Å
R factor r_factor	0.1950
R_work r_work	0.1890
R_free r_free	0.2380

Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5

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

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

Histone H5

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

5wcu__assembly_1__model_1

5wcu__assembly_1__model_1 | I(q)

5wcu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

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

Source Source

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

Source Source

7. Citations (1)