2f8n

2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes

Method: X-RAY DIFFRACTION

▼

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

Histone H3.1

Xenopus laevis

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	alpha-satellite DNA (146 bp) × 2 Histone H4 × 2 （P62799） Histone 3, H2ba × 1 （Q9D2U9） Histone H2B.1 × 1 （P02281） Core histone macro-H2A.1 × 1 （O75367） Histone H2A type 1 × 1 （Q8CGP6） water × 10	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	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 1–135 Author chain E； PDBConstruct 1–136； 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 8 DNA 2	alpha-satellite DNA (146 bp) × 2 Histone H3.1 × 2 （P84233） Histone 3, H2ba × 1 （Q9D2U9） Histone H2B.1 × 1 （P02281） Core histone macro-H2A.1 × 1 （O75367） Histone H2A type 1 × 1 （Q8CGP6） water × 10	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	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–103； UniProt 1–102 Author chain F； PDBConstruct 1–103； UniProt 1–102

Histone 3, H2ba

Mus musculus

UniProt Q9D2U9

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	alpha-satellite DNA (146 bp) × 2 Histone H3.1 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2B.1 × 1 （P02281） Core histone macro-H2A.1 × 1 （O75367） Histone H2A type 1 × 1 （Q8CGP6） water × 10	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B3A_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–126； UniProt 1–125

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 8 DNA 2	alpha-satellite DNA (146 bp) × 2 Histone H3.1 × 2 （P84233） Histone H4 × 2 （P62799） Histone 3, H2ba × 1 （Q9D2U9） Core histone macro-H2A.1 × 1 （O75367） Histone H2A type 1 × 1 （Q8CGP6） water × 10	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	5
Chains and sequence ranges	Author chain H； PDBConstruct 2–123； UniProt 4–125

Core histone macro-H2A.1

Homo sapiens

UniProt O75367

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	alpha-satellite DNA (146 bp) × 2 Histone H3.1 × 2 （P84233） Histone H4 × 2 （P62799） Histone 3, H2ba × 1 （Q9D2U9） Histone H2B.1 × 1 （P02281） Histone H2A type 1 × 1 （Q8CGP6） water × 10	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2AY_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–120； UniProt 1–119

Histone H2A type 1

Mus musculus

UniProt Q8CGP6

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	alpha-satellite DNA (146 bp) × 2 Histone H3.1 × 2 （P84233） Histone H4 × 2 （P62799） Histone 3, H2ba × 1 （Q9D2U9） Histone H2B.1 × 1 （P02281） Core histone macro-H2A.1 × 1 （O75367） water × 10	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1H_MOUSE
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain K； PDBConstruct 20–149； UniProt 1–127

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2f8n
Deposition date deposition_date	2005-12-02
Structure title title	2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes
Keywords keywords	Nucleosome, NCP, macroH2A, Histone variant, chromatin, STRUCTURAL PROTEIN-DNA COMPLEX; STRUCTURAL PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2f8n__assembly_1__model_1

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

Download this curve (.dat)

2f8n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2f8n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.82 Å
Rg (electron density)	37.07 Å
Total Rg	37.79 Å
Atom count	11946
Residues	1048
Excluded volume	194700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2f8n__assembly_1__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	alpha-satellite DNA (146 bp)
Molecular weight formula_weight	45054.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,J
Atom count atom_count	12066

ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT

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 H3.1
Molecular weight formula_weight	15421.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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 3 Entity 3 polymer

Description description	Histone H4
Molecular weight formula_weight	11394.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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 3, H2ba
Molecular weight formula_weight	14025.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MPEPSRSTPAPKKGSKKAITKAQKKDGKKRKRGRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIASEASRLAHYNKRSTITSREVQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Histone H2B.1
Molecular weight formula_weight	13655.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

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	Core histone macro-H2A.1
Molecular weight formula_weight	12984.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MSSRGGKKKSTKTSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVANDEELNQLLKGVTIASGGVLPNIHPELLAKKRGS

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 7 Entity 7 polymer

Description description	Histone H2A type 1
Molecular weight formula_weight	16198.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MGSSHHHHHHSSGLVPRGSMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	120

▼

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2f8na_
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	d2f8nb_
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	d2f8nd_
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	d2f8ne_
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	d2f8nf_
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	d2f8ng_
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	d2f8nh_
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	d2f8nk1
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

CATH v4.4 (8 domains)

Domain ID domain_id	2f8nA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	2f8nB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	2f8nD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	2f8nE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	2f8nF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	2f8nG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	2f8nH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	2f8nK00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

▶

Unit-cell length a length_a	106.145 Å
Unit-cell length b length_b	109.272 Å
Unit-cell length c length_c	176.273 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	31.400 Å
R factor r_factor	—
R_work r_work	0.2170
R_free r_free	0.2690

2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes

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 3, H2ba

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

Core histone macro-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 H2A type 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

2f8n__assembly_1__model_1

2f8n__assembly_1__model_1 | I(q)

2f8n__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 (8)

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