4x23

CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE

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 10 DNA 2	DNA (147-MER) × 1 DNA (147-MER) × 1 Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） CENP-C × 2 （Q66LH7）	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 10 DNA 2	DNA (147-MER) × 1 DNA (147-MER) × 1 Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） CENP-C × 2 （Q66LH7）	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	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–93； UniProt 41–133 Author chain E； PDBConstruct 1–93； UniProt 41–133 Author chain K； PDBConstruct 1–93； UniProt 41–133 Author chain O； PDBConstruct 1–93； UniProt 41–133

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 10 DNA 2	DNA (147-MER) × 1 DNA (147-MER) × 1 Histone H3 × 2 （P02299） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） CENP-C × 2 （Q66LH7）	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 10 DNA 2	DNA (147-MER) × 1 DNA (147-MER) × 1 Histone H3 × 2 （P02299） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） CENP-C × 2 （Q66LH7）	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	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–79； UniProt 25–103 Author chain F； PDBConstruct 1–79； UniProt 25–103 Author chain L； PDBConstruct 1–79； UniProt 25–103 Author chain P； PDBConstruct 1–79； UniProt 25–103

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 10 DNA 2	DNA (147-MER) × 1 DNA (147-MER) × 1 Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2B × 2 （P02283） CENP-C × 2 （Q66LH7）	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 10 DNA 2	DNA (147-MER) × 1 DNA (147-MER) × 1 Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2B × 2 （P02283） CENP-C × 2 （Q66LH7）	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	5
Chains and sequence ranges	Author chain C； PDBConstruct 1–102； UniProt 16–117 Author chain G； PDBConstruct 1–102； UniProt 16–117 Author chain M； PDBConstruct 1–102； UniProt 16–117 Author chain Q； PDBConstruct 1–102； UniProt 16–117

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 10 DNA 2	DNA (147-MER) × 1 DNA (147-MER) × 1 Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） CENP-C × 2 （Q66LH7）	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 10 DNA 2	DNA (147-MER) × 1 DNA (147-MER) × 1 Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） CENP-C × 2 （Q66LH7）	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	6
Chains and sequence ranges	Author chain D； PDBConstruct 1–90； UniProt 33–122 Author chain H； PDBConstruct 1–90； UniProt 33–122 Author chain N； PDBConstruct 1–90； UniProt 33–122 Author chain R； PDBConstruct 1–90； UniProt 33–122

CENP-C

OrganismNot specified

UniProt Q66LH7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 2	DNA (147-MER) × 1 DNA (147-MER) × 1 Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283）	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 10 DNA 2	DNA (147-MER) × 1 DNA (147-MER) × 1 Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q66LH7_RAT
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain U； PDBConstruct 1–25； UniProt 710–734 Author chain V； PDBConstruct 1–25； UniProt 710–734 Author chain W； PDBConstruct 1–25； UniProt 710–734 Author chain X； PDBConstruct 1–25； UniProt 710–734

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	4x23
Deposition date deposition_date	2014-11-25
Structure title title	CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE
Keywords keywords	;NUCLEOSOME CORE PARTICLE, WIDOM 601 DNA FRAGMMENT, HISTONE FOLD, CENP-C COMPLEX, SEGREGATION, CHROMOSOME CENTROMERE, KINETOCHORE ASSEMBLY, CONSTITUTIVE CENTROMERE-ASSOCIATED NETWORK (CCAN) PROTEINS, 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.

4x23__assembly_1__model_1

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

Download this curve (.dat)

4x23__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4x23__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.90 Å
Rg (electron density)	37.02 Å
Total Rg	37.77 Å
Atom count	12011
Residues	1054
Excluded volume	195040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4x23__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4x23__assembly_2__model_1`	dodecameric （12）	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	DNA (147-MER)
Molecular weight formula_weight	45138.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,S
Atom count atom_count	23974

ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGAT

Source Source

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

Entity 2 Entity 2 polymer

Description description	DNA (147-MER)
Molecular weight formula_weight	45610.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J,T

ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAT

Source Source

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

Entity 3 Entity 3 polymer

Description description	Histone H3
Molecular weight formula_weight	11365.3 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

RYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGIEGGL

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 H4
Molecular weight formula_weight	8910.4 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

DNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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	Histone H2A
Molecular weight formula_weight	11093.9 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

SRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLP

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 6 Entity 6 polymer

Description description	Histone H2B
Molecular weight formula_weight	10019.5 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

ESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS

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 7 Entity 7 polymer

Description description	CENP-C
Molecular weight formula_weight	3222.7 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

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

PNVRRSNRIRLKPLEYWRGERIDYQ

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	4x23A00
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	4x23B00
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	4x23C00
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	4x23D00
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	4x23E00
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	4x23F00
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	4x23G00
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	4x23H00
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	4x23K00
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	4x23L00
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	4x23M00
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	4x23N00
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	4x23O00
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	4x23P00
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	4x23Q00
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	4x23R00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

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Unit-cell length a length_a	102.994 Å
Unit-cell length b length_b	176.102 Å
Unit-cell length c length_c	208.846 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	16

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

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	49.543 Å
R factor r_factor	0.2382
R_work r_work	0.2362
R_free r_free	0.2856

CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE

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

CENP-C

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

4x23__assembly_1__model_1

4x23__assembly_1__model_1 | I(q)

4x23__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 (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

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)