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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain K； UniProt 131–239	Not recorded	Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CNN1 × 1 （P43618） Inner kinetochore subunit WIP1 × 1 （Q2V2P8） Inner kinetochore subunit CTF3 × 1 （Q12748）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；1 M NaH2PO4 and 0.38M K2HPO4 with protein at 5.5 mg/ml	Resolution 2.90 Å R-free 0.283

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6YPC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6OUA Cryo-EM structure of the yeast Ctf3 complex Deposited 2019-05-04	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1–239（239 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.18 Å
6QLD Structure of inner kinetochore CCAN-Cenp-A complex Deposited 2019-01-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain K 7–128（122 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.15 Å
6QLE Structure of inner kinetochore CCAN complex Deposited 2019-01-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain K 1–133（133 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.55 Å
6WUC The yeast Ctf3 complex with Cnn1-Wip1 Deposited 2020-05-04	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain K 1–239（239 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
7L7Q Ctf3c with Ulp2-KIM Deposited 2020-12-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1–239（239 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain K 1–239（239 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain K 1–239（239 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric	Chain K 1–239（239 aa） Chain KK 1–239（239 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain H； UniProt 137–181	Not recorded	Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit CNN1 × 1 （P43618） Inner kinetochore subunit WIP1 × 1 （Q2V2P8） Inner kinetochore subunit CTF3 × 1 （Q12748）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；1 M NaH2PO4 and 0.38M K2HPO4 with protein at 5.5 mg/ml	Resolution 2.90 Å R-free 0.283

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6YPC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6OUA Cryo-EM structure of the yeast Ctf3 complex Deposited 2019-05-04	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–181（181 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.18 Å
6QLD Structure of inner kinetochore CCAN-Cenp-A complex Deposited 2019-01-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain H 4–136（133 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.15 Å
6WUC The yeast Ctf3 complex with Cnn1-Wip1 Deposited 2020-05-04	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 1–181（181 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
7L7Q Ctf3c with Ulp2-KIM Deposited 2020-12-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–181（181 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain H 1–181（181 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain H 1–181（181 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric	Chain H 1–181（181 aa） Chain HH 1–181（181 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain T； UniProt 1–361	Not recorded	Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit WIP1 × 1 （Q2V2P8） Inner kinetochore subunit CTF3 × 1 （Q12748）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；1 M NaH2PO4 and 0.38M K2HPO4 with protein at 5.5 mg/ml	Resolution 2.90 Å R-free 0.283

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6YPC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4GEQ Crystal structure of the Spc24-Spc25/Cnn1 binding interface Deposited 2012-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 60–84（25 aa） Fragment：Cnn1p N-terminal motif, residues 60-84	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293.15 K；15% PEG6000, 5% glycerol; Drop volume: 0.2ul; Protein proportion: 50%; Protein concentration: 6 mg/ml, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.01 Å R-free 0.258
4GEQ Crystal structure of the Spc24-Spc25/Cnn1 binding interface Deposited 2012-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 60–84（25 aa） Fragment：Cnn1p N-terminal motif, residues 60-84	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293.15 K；15% PEG6000, 5% glycerol; Drop volume: 0.2ul; Protein proportion: 50%; Protein concentration: 6 mg/ml, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.01 Å R-free 0.258
6WUC The yeast Ctf3 complex with Cnn1-Wip1 Deposited 2020-05-04	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain T 1–361（361 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain T 1–361（361 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain T 1–361（361 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric	Chain T 1–361（361 aa） Chain TT 1–361（361 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain W； UniProt 1–89	Not recorded	Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CNN1 × 1 （P43618） Inner kinetochore subunit CTF3 × 1 （Q12748）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；1 M NaH2PO4 and 0.38M K2HPO4 with protein at 5.5 mg/ml	Resolution 2.90 Å R-free 0.283

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6YPC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6WUC The yeast Ctf3 complex with Cnn1-Wip1 Deposited 2020-05-04	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain W 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain W 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain W 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric	Chain W 1–89（89 aa） Chain WW 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain I； UniProt 1–245	Not recorded	Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CNN1 × 1 （P43618） Inner kinetochore subunit WIP1 × 1 （Q2V2P8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；1 M NaH2PO4 and 0.38M K2HPO4 with protein at 5.5 mg/ml	Resolution 2.90 Å R-free 0.283

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6YPC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6NUW Yeast Ctf19 complex Deposited 2019-02-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain H 1–733（733 aa） Chain Y 1–733（733 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.25 Å
6OUA Cryo-EM structure of the yeast Ctf3 complex Deposited 2019-05-04	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1–733（733 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.18 Å
6QLD Structure of inner kinetochore CCAN-Cenp-A complex Deposited 2019-01-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain I 321–728（408 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.15 Å
6QLE Structure of inner kinetochore CCAN complex Deposited 2019-01-31	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain I 335–656（322 aa） Chain I 690–733（44 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.55 Å
6WUC The yeast Ctf3 complex with Cnn1-Wip1 Deposited 2020-05-04	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 1–733（733 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
7L7Q Ctf3c with Ulp2-KIM Deposited 2020-12-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1–733（733 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain I 1–733（733 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain I 1–733（733 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric	Chain I 1–733（733 aa） Chain II 1–733（733 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	26.57 Å
Radius of gyration Rg (electron density) rg_electron	25.47 Å
Forward intensity I(0) i0	57385500.00
Molecular weight molecular_weight	61536.0 kDa
Excluded volume excluded_volume	78295 Å³
Envelope volume envelope_volume	95272 Å³
Hydration-shell volume shell_volume	31040 Å³
Envelope diameter envelope_diameter	86.2 Å
Shell Rg shell_rg	32.90 Å
Envelope Rg envelope_rg	25.64 Å
Shape Rg shape_rg	25.45 Å
Total Rg total_rg	26.39 Å
Total atoms total_atoms	4334
Residues n_residues	535
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	83.0 Å
Rg (real space) rg_real	26.47 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	5.7390e+07
I(0) uncertainty (real space) i0_real_error	7.9620e+05
Rg (reciprocal space) rg_reciprocal	26.50 Å
I(0) (reciprocal space) i0_reciprocal	57390000.0000
Solution quality estimate total_estimate	0.9067
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.8 Å
Skewness Skewness skewness	0.230
Kurtosis Kurtosis kurtosis	-0.430
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11820000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 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

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 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

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 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

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 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

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/yp/6ypc/6ypc.fit
pddf	/app/data/pr_computation/yp/6ypc/6ypc.pr.out
profile	/app/data/saxs_computation/yp/6ypc/6ypc.dat

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

Inner kinetochore subunit MCM16

State in the Current Structure

Other States of the Same Protein in the Database

Inner kinetochore subunit CNN1

State in the Current Structure

Other States of the Same Protein in the Database

Inner kinetochore subunit WIP1

State in the Current Structure

Other States of the Same Protein in the Database

Inner kinetochore subunit CTF3

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)