9lrv

Cryo-EM structure of Fission yeast centromeric nucleosome Class 1

Method: ELECTRON MICROSCOPY

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

Histone H3-like centromeric protein cnp1

Schizosaccharomyces pombe (strain 972 / ATCC 24843)

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	Histone H4 × 2 （P09322） Histone H2A-alpha × 2 （P04909） Histone H2B-alpha × 2 （P04913） DNA (144-MER) × 1 DNA (144-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CENPA_SCHPO
Isoform	—
PDB entities	1, 5
Chains and sequence ranges	Author chain A； PDBConstruct 7–126； UniProt 1–120 Author chain E； PDBConstruct 1–120； UniProt 1–120

Histone H4

Schizosaccharomyces pombe (strain 972 / ATCC 24843)

UniProt P09322

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	Histone H3-like centromeric protein cnp1 × 1 （Q9Y812） Histone H2A-alpha × 2 （P04909） Histone H2B-alpha × 2 （P04913） Histone H3-like centromeric protein cnp1 × 1 （Q9Y812） DNA (144-MER) × 1 DNA (144-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_SCHPO
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-alpha

Schizosaccharomyces pombe (strain 972 / ATCC 24843)

UniProt P04909

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	Histone H3-like centromeric protein cnp1 × 1 （Q9Y812） Histone H4 × 2 （P09322） Histone H2B-alpha × 2 （P04913） Histone H3-like centromeric protein cnp1 × 1 （Q9Y812） DNA (144-MER) × 1 DNA (144-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1_SCHPO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–132； UniProt 1–132 Author chain G； PDBConstruct 1–132； UniProt 1–132

Histone H2B-alpha

Schizosaccharomyces pombe (strain 972 / ATCC 24843)

UniProt P04913

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	Histone H3-like centromeric protein cnp1 × 1 （Q9Y812） Histone H4 × 2 （P09322） Histone H2A-alpha × 2 （P04909） Histone H3-like centromeric protein cnp1 × 1 （Q9Y812） DNA (144-MER) × 1 DNA (144-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B1_SCHPO
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

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	9lrv
Deposition date deposition_date	2025-02-01
Structure title title	Cryo-EM structure of Fission yeast centromeric nucleosome Class 1
Keywords keywords	Nucleosome dynamics, CENP-A, Cnp1, kinetochore assembly, Chromosome Segregation, NUCLEAR PROTEIN/DNA, NUCLEAR PROTEIN-DNA complex; NUCLEAR PROTEIN/DNA
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.

9lrv__assembly_1__model_1

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

Download this curve (.dat)

9lrv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9lrv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.06 Å
Rg (electron density)	37.28 Å
Total Rg	38.01 Å
Atom count	11645
Residues	1030
Excluded volume	188460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9lrv__assembly_1__model_1`	decameric （10）	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 cnp1
Molecular weight formula_weight	14737.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	11645

HHHHHHMAKKSLMAEPGDPIPRPRKKRYRPGTTALREIRKYQRSTDLLIQRLPFSRIVREISSEFVANFSTDVGLRWQSTALQCLQEAAEAFLVHLFEDTNLCAIHAKRVTIMQRDMQLARRIRGA

Source Source

Source organism organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	in vitro transcription vector pT7-Fluc(deltai)

Entity 2 Entity 2 polymer

Description description	Histone H4
Molecular weight formula_weight	11450.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISALVYEETRAVLKLFLENVIRDAVTYTEHAKRKTVTSLDVVYSLKRQGRTIYGFGG

Source Source

Source organism organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	in vitro transcription vector pT7-Fluc(deltai)

Entity 3 Entity 3 polymer

Description description	Histone H2A-alpha
Molecular weight formula_weight	13902.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSGGKSGGKAAVAKSAQSRSAKAGLAFPVGRVHRLLRKGNYAQRVGAGAPVYLAAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGHVTIAQGGVVPNINAHLLPKTSGRTGKPSQEL

Source Source

Source organism organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	in vitro transcription vector pT7-Fluc(deltai)

Entity 4 Entity 4 polymer

Description description	Histone H2B-alpha
Molecular weight formula_weight	13844.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSAAEKKPASKAPAGKAPRDTMKSADKKRGKNRKETYSSYIYKVLKQVHPDTGISNQAMRILNSFVNDIFERIATEASKLAAYNKKSTISSREIQTAVRLILPGELAKHAVTEGTKSVTKYSSSAQ

Source Source

Source organism organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	in vitro transcription vector pT7-Fluc(deltai)

Entity 5 Entity 5 polymer

Description description	Histone H3-like centromeric protein cnp1
Molecular weight formula_weight	13908.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MAKKSLMAEPGDPIPRPRKKRYRPGTTALREIRKYQRSTDLLIQRLPFSRIVREISSEFVANFSTDVGLRWQSTALQCLQEAAEAFLVHLFEDTNLCAIHAKRVTIMQRDMQLARRIRGA

Source Source

Source organism organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	in vitro transcription vector pT7-Fluc(deltai)

Entity 6 Entity 6 polymer

Description description	DNA (144-MER)
Molecular weight formula_weight	45098.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCACATATATACATCCGAT

Source Source

Source organism organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	in vitro transcription vector pT7-Fluc(deltai)

Entity 7 Entity 7 polymer

Description description	DNA (144-MER)
Molecular weight formula_weight	45650.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

ATCGGATGTATATATGTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAT

Source Source

Source organism organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	in vitro transcription vector pT7-Fluc(deltai)

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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	2.990 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.99 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	429911

Cryo-EM structure of Fission yeast centromeric nucleosome Class 1

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

Histone H3-like centromeric protein cnp1

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-alpha

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-alpha

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

9lrv__assembly_1__model_1

9lrv__assembly_1__model_1 | I(q)

9lrv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

7. Citations (1)