SAXSdb — 6ypc

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

Inner kinetochore subunit MCM22

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CNN1 × 1 （P43618） Inner kinetochore subunit WIP1 × 1 （Q2V2P8） Inner kinetochore subunit CTF3 × 1 （Q12748） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CENPK_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain K； PDBConstruct 2–110； UniProt 131–239

Inner kinetochore subunit MCM16

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q12262

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit CNN1 × 1 （P43618） Inner kinetochore subunit WIP1 × 1 （Q2V2P8） Inner kinetochore subunit CTF3 × 1 （Q12748） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CENPH_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 2–46； UniProt 137–181

Inner kinetochore subunit CNN1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P43618

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit WIP1 × 1 （Q2V2P8） Inner kinetochore subunit CTF3 × 1 （Q12748） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CENPT_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain T； PDBConstruct 1–361； UniProt 1–361

Inner kinetochore subunit WIP1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q2V2P8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CNN1 × 1 （P43618） Inner kinetochore subunit CTF3 × 1 （Q12748） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CENPW_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain W； PDBConstruct 1–89； UniProt 1–89

Inner kinetochore subunit CTF3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q12748

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CNN1 × 1 （P43618） Inner kinetochore subunit WIP1 × 1 （Q2V2P8） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CENPI_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain I； PDBConstruct 1–245； UniProt 1–245

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	6ypc
Deposition date deposition_date	2020-04-15
Structure title title	Crystal structure of the kinetochore subunits H/I/K/T/W penta-complex from S. cerevisiae at 2.9 angstroms
Keywords keywords	kinetochore, cenp complex, centromeres, chromosome segregation, CELL CYCLE; CELL CYCLE
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.

6ypc__assembly_1__model_1

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

Download this curve (.dat)

6ypc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ypc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.57 Å
Rg (electron density)	25.47 Å
Total Rg	26.39 Å
Atom count	4334
Residues	535
Excluded volume	78295 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ypc__assembly_1__model_1`	pentameric （5）	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 (6)

Entity 1 Entity 1 polymer

Description description	Inner kinetochore subunit MCM22
Molecular weight formula_weight	12748.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K
Atom count atom_count	4341

MKKQDHAHIRTRKARNKELWDSLADFLKGYLVPNLDDNDESIDSLTNEVMLLMKRLIEHDLNLTLNDFSSKTIPIYRLLLRANIITVIEGSTNPGTKYIKLIDFNETSLT

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Inner kinetochore subunit MCM16
Molecular weight formula_weight	5153.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MKPTIPPDDSDTAGKQVEVEKENETIQELMIALQIHSGYTNISYTI

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Inner kinetochore subunit CNN1
Molecular weight formula_weight	42154.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T

MSTPRKAAGNNENTEVSEIRTPFRERALEEQRLKDEVLIRNTPGYRKLLSASTKSHDILNKDPNEVRSFLQDLSQVLARKSQGNDTTTNKTQARNLIDELAYEESQPEENELLRSRSEKLTDNNIGNETQPDYTSLSQTVFAKLQERDKGLKSRKIDPIIIQDVPTTGHEDELTVHSPDKANSISMEVLRTSPSIGMDQVDEPPVRDPVPISITQQEEPLSEDLPSDDKEETEEAENEDYSFENTSDENLDDIGNDPIRLNVPAVRRSSIKPLQIMDLKHLTRQFLNENRIILPKQTWSTIQEESLNIMDFLKQKIGTLQKQELVDSFIDMGIINNVDDMFELAHELLPLELQSRIESYLFENLYFQ

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Inner kinetochore subunit WIP1
Molecular weight formula_weight	10255.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W

MDTEALANYLLRQLSLDAEENKLEDLLQRQNEDQESSQEYNKKLLLACGFQAILRKILLDARTRATAEGLREVYPYHIEAATQAFLDSQ

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Inner kinetochore subunit CTF3
Molecular weight formula_weight	28856.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MSLILDDIILSLTNANERTPPQALKTTLSLLYEKSKQYGLSSPQLQALVRLLCETSIIDTVTKVYIVENCFLPDGYLTKELLLEIINHLGTPTVFSRYRIQTPPVLQSALCKWLVHVYFLFPVHSEREHNISSSIWLHLWQFSFLQKWITPLVIWQATTPVDVKPWKLSIIKRCAMHPGYRDAPGSATLILQRFQCLVGASSQITESIITINCNRKTLKSHRNLKLDAHFLSILKRILSRAHPANENLYFQ

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	7

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Unit-cell length a length_a	132.577 Å
Unit-cell length b length_b	132.577 Å
Unit-cell length c length_c	241.676 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	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	tetragonal

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	68.850 Å
R factor r_factor	0.2312
R_work r_work	0.2283
R_free r_free	0.2829

Crystal structure of the kinetochore subunits H/I/K/T/W penta-complex from S. cerevisiae at 2.9 angstroms

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

Inner kinetochore subunit MCM22

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Inner kinetochore subunit MCM16

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Inner kinetochore subunit CNN1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Inner kinetochore subunit WIP1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Inner kinetochore subunit CTF3

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

6ypc__assembly_1__model_1

6ypc__assembly_1__model_1 | I(q)

6ypc__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 (6)

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 water

7. Citations (1)