5z23

Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD

Method: X-RAY DIFFRACTION

▼

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

Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8 DNA 2	Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 1-J × 2 （P06899） DNA (146-MER) × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CENPA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 79–118； UniProt 75–114 Author chain E； PDBConstruct 79–118； UniProt 75–114

Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1

Homo sapiens

UniProt P68431

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8 DNA 2	Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 1-J × 2 （P06899） DNA (146-MER) × 2	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 4–78； UniProt 1–75 Author chain A； PDBConstruct 119–141； UniProt 114–136 Author chain E； PDBConstruct 4–78； UniProt 1–75 Author chain E； PDBConstruct 119–141； UniProt 114–136

Histone H4

Homo sapiens

UniProt P62805

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8 DNA 2	Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1 × 2 （P49450,P68431） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 1-J × 2 （P06899） DNA (146-MER) × 2	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 4–106； UniProt 1–103 Author chain F； PDBConstruct 4–106； 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	Insufficient information	Heteromer	Protein 8 DNA 2	Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1 × 2 （P49450,P68431） Histone H4 × 2 （P62805） Histone H2B type 1-J × 2 （P06899） DNA (146-MER) × 2	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 4–133； UniProt 1–130 Author chain G； PDBConstruct 4–133； 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	Insufficient information	Heteromer	Protein 8 DNA 2	Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1 × 2 （P49450,P68431） Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 2 （P04908） DNA (146-MER) × 2	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 4–129； UniProt 1–126 Author chain H； PDBConstruct 4–129； UniProt 1–126

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	5z23
Deposition date deposition_date	2017-12-28
Structure title title	Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD
Keywords keywords	Nucleosome, Chromosome, CENP-A, centromere, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING 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.

5z23__assembly_1__model_1

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

Download this curve (.dat)

5z23__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5z23__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.73 Å
Rg (electron density)	37.01 Å
Total Rg	37.68 Å
Atom count	12007
Residues	1037
Excluded volume	195800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5z23__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 (5)

Entity 1 Entity 1 polymer

Description description	Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1
Molecular weight formula_weight	16063.9 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	12007

GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAKRVTIMPKDIQLARRIRGERA

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Histone H4
Molecular weight formula_weight	11676.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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	18406.7 kDa
Mutation mutation	L51M,L58M,L93M
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYMAAVLEYMTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEEMNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGKQLAIRNDEEMNKLLGRVTIAQGGVLPNIQAVLLP

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	14358.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

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 (146-MER)
Molecular weight formula_weight	45053.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,J

ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

▼

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d5z23b_
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	d5z23c_
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	d5z23d_
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	d5z23f_
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	d5z23g_
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	d5z23h_
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	5z23A00
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	5z23B00
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	5z23C00
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	5z23D00
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	5z23E00
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	5z23F00
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	5z23G00
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	5z23H00
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	99.641 Å
Unit-cell length b length_b	100.745 Å
Unit-cell length c length_c	173.431 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	2.730 Å
Low-resolution limit resolution_low	47.884 Å
R factor r_factor	0.2055
R_work r_work	0.2029
R_free r_free	0.2614

Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD

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

Histone H3.1,Histone H3-like centromeric protein A,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 H3.1,Histone H3-like centromeric protein A,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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5z23__assembly_1__model_1

5z23__assembly_1__model_1 | I(q)

5z23__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 (5)

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

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)