7xvm

Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment)

Method: X-RAY DIFFRACTION

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

Histone H3.1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 18 DNA 4	Histone H4 × 4 （P62805） Histone H2A type 1-B/E × 4 （P04908） Histone H2B type 1-J × 4 （P06899） DNA (169-MER) × 2 DNA (169-MER) × 2 Histone H5 × 2 （P02259） CALCIUM ION × 18 CHLORIDE ION × 3 POTASSIUM ION × 2 water × 9	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H31_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–138； UniProt 1–136 Author chain E； PDBConstruct 3–138； UniProt 1–136 Author chain K； PDBConstruct 3–138； UniProt 1–136 Author chain O； PDBConstruct 3–138； UniProt 1–136

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 18 DNA 4	Histone H3.1 × 4 （P68431） Histone H2A type 1-B/E × 4 （P04908） Histone H2B type 1-J × 4 （P06899） DNA (169-MER) × 2 DNA (169-MER) × 2 Histone H5 × 2 （P02259） CALCIUM ION × 18 CHLORIDE ION × 3 POTASSIUM ION × 2 water × 9	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 3–105； UniProt 1–103 Author chain F； PDBConstruct 3–105； UniProt 1–103 Author chain L； PDBConstruct 3–105； UniProt 1–103 Author chain P； PDBConstruct 3–105； UniProt 1–103

Histone H2A type 1-B/E

Homo sapiens

UniProt P04908

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 18 DNA 4	Histone H3.1 × 4 （P68431） Histone H4 × 4 （P62805） Histone H2B type 1-J × 4 （P06899） DNA (169-MER) × 2 DNA (169-MER) × 2 Histone H5 × 2 （P02259） CALCIUM ION × 18 CHLORIDE ION × 3 POTASSIUM ION × 2 water × 9	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1B_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 3–132； UniProt 1–130 Author chain G； PDBConstruct 3–132； UniProt 1–130 Author chain M； PDBConstruct 3–132； UniProt 1–130 Author chain Q； PDBConstruct 3–132； UniProt 1–130

Histone H2B type 1-J

Homo sapiens

UniProt P06899

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 18 DNA 4	Histone H3.1 × 4 （P68431） Histone H4 × 4 （P62805） Histone H2A type 1-B/E × 4 （P04908） DNA (169-MER) × 2 DNA (169-MER) × 2 Histone H5 × 2 （P02259） CALCIUM ION × 18 CHLORIDE ION × 3 POTASSIUM ION × 2 water × 9	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B1J_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 3–128； UniProt 1–126 Author chain H； PDBConstruct 3–128； UniProt 1–126 Author chain N； PDBConstruct 3–128； UniProt 1–126 Author chain R； PDBConstruct 3–128； UniProt 1–126

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 18 DNA 4	Histone H3.1 × 4 （P68431） Histone H4 × 4 （P62805） Histone H2A type 1-B/E × 4 （P04908） Histone H2B type 1-J × 4 （P06899） DNA (169-MER) × 2 DNA (169-MER) × 2 CALCIUM ION × 18 CHLORIDE ION × 3 POTASSIUM ION × 2 water × 9	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 2–190； UniProt 2–190 Author chain V； PDBConstruct 2–190； UniProt 2–190

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	7xvm
Deposition date deposition_date	2022-05-24
Structure title title	Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment)
Keywords keywords	;linker histone, nucleosome binding, chromatin structure, chromatin compaction, histone variants, STRUCTURAL PROTEIN-DNA complex, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex ;; DNA 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.

7xvm__assembly_1__model_1

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

Download this curve (.dat)

7xvm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7xvm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	78.16 Å
Rg (electron density)	78.97 Å
Total Rg	78.91 Å
Atom count	27682
Residues	2417
Excluded volume	450300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7xvm__assembly_1__model_1`	22-meric （22）	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 (11)

Entity 1 Entity 1 polymer

Description description	Histone H3.1
Molecular weight formula_weight	15581.3 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	27693

GSMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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	11538.6 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

GSMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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 1-B/E
Molecular weight formula_weight	14309.7 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

GSMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

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-J
Molecular weight formula_weight	14079.4 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

GSMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

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	DNA (169-MER)
Molecular weight formula_weight	52173.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,S

GCTTTTTTTTTTCACAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGGAATCCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTGTGAAAAAAAAAAGCTGCA

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	DNA (169-MER)
Molecular weight formula_weight	52164.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J,T

GCTTTTTTTTTTCACAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGGATTCCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTGTGAAAAAAAAAAGCTGCA

Source Source

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

Entity 7 Entity 7 polymer

Description description	Histone H5
Molecular weight formula_weight	20758.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

STESLVLSPAPAKPKRVKASRRSASHPTYSEMIAAAIRAEKSRGGSSRQSIQKYIKSHYKVGHNADLQIKLSIRRLLAAGVLKQTKGVGASGSFRLAKSDKAKRSPGKKKKAVRRSTSPKKAARPRKARSPAKKPKATARKARKKSRASPKKAKKPKTVKAKSRKASKAKKVKRSKPRAKSGARKSPKKK

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

Entity 8 Entity 8 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 9 Entity 9 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	11

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Unit-cell length a length_a	105.160 Å
Unit-cell length b length_b	103.758 Å
Unit-cell length c length_c	212.955 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.840 Å
Low-resolution limit resolution_low	48.030 Å
R factor r_factor	0.2016
R_work r_work	0.2004
R_free r_free	0.2590

Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment)

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

Histone H3.1

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 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 1-B/E

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-J

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

7xvm__assembly_1__model_1

7xvm__assembly_1__model_1 | I(q)

7xvm__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 (11)

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

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

7. Citations (1)