7r5r

Structure of the human CCAN CENP-A alpha-satellite complex

Method: ELECTRON MICROSCOPY

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

Histone H3-like centromeric protein A

Homo sapiens

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	Histone H4 × 2 （P62805） Histone H2A type 1-C × 2 （Q93077） Histone H2B type 1-C/E/F/G/I × 2 （P62807） DNA (171-MER) × 1 DNA (171-MER) × 1 Centromere protein C × 2 （Q03188）	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 1–140； UniProt 1–140 Author chain E； PDBConstruct 1–140； UniProt 1–140

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 10 DNA 2	Histone H3-like centromeric protein A × 2 （P49450） Histone H2A type 1-C × 2 （Q93077） Histone H2B type 1-C/E/F/G/I × 2 （P62807） DNA (171-MER) × 1 DNA (171-MER) × 1 Centromere protein C × 2 （Q03188）	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 1–103； UniProt 1–103 Author chain F； PDBConstruct 1–103； UniProt 1–103

Histone H2A type 1-C

Homo sapiens

UniProt Q93077

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	Histone H3-like centromeric protein A × 2 （P49450） Histone H4 × 2 （P62805） Histone H2B type 1-C/E/F/G/I × 2 （P62807） DNA (171-MER) × 1 DNA (171-MER) × 1 Centromere protein C × 2 （Q03188）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1C_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–130； UniProt 1–130 Author chain G； PDBConstruct 1–130； UniProt 1–130

Histone H2B type 1-C/E/F/G/I

Homo sapiens

UniProt P62807

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	Histone H3-like centromeric protein A × 2 （P49450） Histone H4 × 2 （P62805） Histone H2A type 1-C × 2 （Q93077） DNA (171-MER) × 1 DNA (171-MER) × 1 Centromere protein C × 2 （Q03188）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B1C_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–126； UniProt 1–126 Author chain H； PDBConstruct 1–126； UniProt 1–126

Centromere protein C

Homo sapiens

UniProt Q03188

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	Histone H3-like centromeric protein A × 2 （P49450） Histone H4 × 2 （P62805） Histone H2A type 1-C × 2 （Q93077） Histone H2B type 1-C/E/F/G/I × 2 （P62807） DNA (171-MER) × 1 DNA (171-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CENPC_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain K； PDBConstruct 1–543； UniProt 2–544 Author chain L； PDBConstruct 1–543； UniProt 2–544

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	7r5r
Deposition date deposition_date	2022-02-11
Structure title title	Structure of the human CCAN CENP-A alpha-satellite complex
Keywords keywords	Chromosome, kinetochore, cell division, centromere, CELL CYCLE; CELL CYCLE
Experimental Method method	ELECTRON MICROSCOPY

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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.

7r5r__assembly_1__model_1

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

Download this curve (.dat)

7r5r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7r5r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.91 Å
Rg (electron density)	37.04 Å
Total Rg	37.84 Å
Atom count	11625
Residues	1045
Excluded volume	190560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7r5r__assembly_1__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	Histone H3-like centromeric protein A
Molecular weight formula_weight	16023.6 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	11625

MGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSRRRQGWLKEIRKLQKSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGLEEGLG

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	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	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-C
Molecular weight formula_weight	14135.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

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-C/E/F/G/I
Molecular weight formula_weight	13937.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

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 (171-MER)
Molecular weight formula_weight	52725.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

TCCAAATGTCCAATTCCAGATACTACAAAAAGAGTGTTTCAAAACTGCTCTATGAAAAGGAATGTTCAACTCTATGAGTTGAATGCAAACATCACATAGAAGTTTCTGAGAATGCTTCTGTCTAGTTTTTATGTGAACATATTCCCGTTTCCAACGAAGGCCTCAAAGCGG

Entity 6 Entity 6 polymer

Description description	DNA (171-MER)
Molecular weight formula_weight	52822.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

CCGCTTTGAGGCCTTCGTTGGAAACGGGAATATGTTCACATAAAAACTAGACAGAAGCATTCTCAGAAACTTCTATGTGATGTTTGCATTCAACTCATAGAGTTGAACATTCCTTTTCATAGAGCAGTTTTGAAACACTCTTTTTGTAGTATCTGGAATTGGACATTTGGA

Entity 7 Entity 7 polymer

Description description	Centromere protein C
Molecular weight formula_weight	61724.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,L

AASGLDHLKNGYRRRFCRPSRARDINTEQGQNVLEILQDCFEEKSLANDFSTNSTKSVPNSTRKIKDTCIQSPSKECQKSHPKSVPVSSKKKEASLQFVVEPSEATNRSVQAHEVHQKILATDVSSKNTPDSKKISSRNINDHHSEADEEFYLSVGSPSVLLDAKTSVSQNVIPSSAQKRETYTFENSVNMLPSSTEVSVKTKKRLNFDDKVMLKKIEIDNKVSDEEDKTSEGQERKPSGSSQNRIRDSEYEIQRQAKKSFSTLFLETVKRKSESSPIVRHAATAPPHSCPPDDTKLIEDEFIIDESDQSFASRSWITIPRKAGSLKQRTISPAESTALLQGRKSREKHHNILPKTLANDKHSHKPHPVETSQPSDKTVLDTSYALIGETVNNYRSTKYEMYSKNAEKPSRSKRTIKQKQRRKFMAKPAEEQLDVGQSKDENIHTSHITQDEFQRNSDRNMEEHEEMGNDCVSKKQMPPVGSKKSSTRKDKEESKKKRFSSESKNKLVPEEVTSTVTKSRRISRRPSDWWVVKSEESPVYSNS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.44 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	189204

Structure of the human CCAN CENP-A alpha-satellite complex

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

Histone H3-like centromeric protein A

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-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

Histone H2B type 1-C/E/F/G/I

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Centromere protein 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

7r5r__assembly_1__model_1

7r5r__assembly_1__model_1 | I(q)

7r5r__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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)