SAXSdb — 6gyu

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

Centromere DNA-binding protein complex CBF3 subunit B

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 B； UniProt 1–608 Chain C； UniProt 49–608	Not recorded	Centromere DNA-binding protein complex CBF3 subunit C × 1 （P35203） Suppressor of kinetochore protein 1 × 1 （P52286） Centromere DNA-binding protein complex CBF3 subunit A × 1 （P32504） ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

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 6GYU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2QUQ Crystal Structure of the Essential Inner Kinetochore Protein Cep3p Deposited 2007-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 47–608（562 aa） Fragment：residues 47-608	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100 mM HEPES, 5% PEG 4000, 500 mM NaCl, pH 7.5, vapor diffusion, hanging drop, temperature 298K	Resolution 2.80 Å R-free 0.285
2VEQ Insights into kinetochore-DNA interactions from the structure of Cep3p Deposited 2007-10-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 48–608（561 aa） Fragment：RESIDUES 48-608	Not recorded	BME BETA-MERCAPTOETHANOL × 2 CAC CACODYLATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；100MM SODIUM CACODYLATE PH 6.5, 0.2M POTASSIUM THIOCYANATE, 12% PEG 4000	Resolution 2.49 Å R-free 0.246
6F07 CBF3 Core Complex Deposited 2017-11-17	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–608（608 aa） Chain B 1–608（608 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6FE8 Cryo-EM structure of the core Centromere Binding Factor 3 complex Deposited 2017-12-30	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 47–608（562 aa） Chain B 47–608（562 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6GSA Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10 Deposited 2018-06-13	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: tetrameric	Chain A 47–608（562 aa） Chain B 47–608（562 aa）	Mutation：Truncation of the N-terminal domain, UNP residues 1-46 Mutation：Truncation of the N-terminal domain, UNP residues 1-46	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6GYP Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore Deposited 2018-07-01	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–608（608 aa） Chain C 49–608（560 aa）	Not recorded	MET METHIONINE × 1 PHE PHENYLALANINE × 1 ASN ASPARAGINE × 1 ARG ARGININE × 1 THR THREONINE × 2 GLN GLUTAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6GYS Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore Deposited 2018-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain B 1–608（608 aa） Chain C 1–608（608 aa） Chain I 1–608（608 aa） Chain J 1–608（608 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
7K79 CBF3 Deposited 2020-09-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 1–608（608 aa） Chain O 1–608（608 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7K7G nucleosome and Gal4 complex Deposited 2020-09-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain M 1–48（48 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric	Chain CE 1–608（608 aa） Chain ce 1–608（608 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

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CBF3B_YEAST
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain B； PDBConstruct 1–608； UniProt 1–608 Author chain C； PDBConstruct 5–564； UniProt 49–608

Centromere DNA-binding protein complex CBF3 subunit C

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P35203

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 A； UniProt 1–478	Not recorded	Centromere DNA-binding protein complex CBF3 subunit B × 1 （P40969） Centromere DNA-binding protein complex CBF3 subunit B × 1 （P40969） Suppressor of kinetochore protein 1 × 1 （P52286） Centromere DNA-binding protein complex CBF3 subunit A × 1 （P32504） ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

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 6GYU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6FE8 Cryo-EM structure of the core Centromere Binding Factor 3 complex Deposited 2017-12-30	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 2–478（477 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6GSA Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10 Deposited 2018-06-13	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: tetrameric	Chain D 2–478（477 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6GYP Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore Deposited 2018-07-01	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–478（478 aa）	Not recorded	MET METHIONINE × 1 PHE PHENYLALANINE × 1 ASN ASPARAGINE × 1 ARG ARGININE × 1 THR THREONINE × 2 GLN GLUTAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6GYS Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore Deposited 2018-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain A 1–478（478 aa） Chain H 1–478（478 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
7K79 CBF3 Deposited 2020-09-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain K 2–478（477 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric	Chain CT 1–478（478 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

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

View Construct and Data Evidence

UniProt name	CBF3C_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–478； UniProt 1–478

Suppressor of kinetochore protein 1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P52286

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 D； UniProt 1–194	Not recorded	Centromere DNA-binding protein complex CBF3 subunit B × 1 （P40969） Centromere DNA-binding protein complex CBF3 subunit C × 1 （P35203） Centromere DNA-binding protein complex CBF3 subunit B × 1 （P40969） Centromere DNA-binding protein complex CBF3 subunit A × 1 （P32504） ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

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 6GYU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NEX Crystal Structure of ScSkp1-ScCdc4-CPD peptide complex Deposited 2002-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–193（193 aa） Fragment：residues 36-63 deleted	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Ammonium Sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.273
1NEX Crystal Structure of ScSkp1-ScCdc4-CPD peptide complex Deposited 2002-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–193（193 aa） Fragment：residues 36-63 deleted	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Ammonium Sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.273
3MKS Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2 Deposited 2010-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–194（193 aa） Fragment：UNP Residues 2-194 with 37-64 deleted Chain C 2–194（193 aa） Fragment：UNP Residues 2-194 with 37-64 deleted	Not recorded	SO4 SULFATE ION × 11 C1C 1,1'-binaphthalene-2,2'-dicarboxylic acid × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；1.5 M Ammonium sulfate, 100mM Tris pH 8.5, 15% glycerol, 1mM SCF-I2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.266
3MKS Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2 Deposited 2010-04-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–194（193 aa） Fragment：UNP Residues 2-194 with 37-64 deleted	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；1.5 M Ammonium sulfate, 100mM Tris pH 8.5, 15% glycerol, 1mM SCF-I2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.266
3MKS Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2 Deposited 2010-04-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–194（193 aa） Fragment：UNP Residues 2-194 with 37-64 deleted	Not recorded	SO4 SULFATE ION × 6 C1C 1,1'-binaphthalene-2,2'-dicarboxylic acid × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；1.5 M Ammonium sulfate, 100mM Tris pH 8.5, 15% glycerol, 1mM SCF-I2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.266
3V7D Crystal Structure of ScSkp1-ScCdc4-pSic1 peptide complex Deposited 2011-12-20	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–194（194 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5 M Ammonium Sulphate, 0.1 M Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.31 Å R-free 0.221
3V7D Crystal Structure of ScSkp1-ScCdc4-pSic1 peptide complex Deposited 2011-12-20	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–194（194 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5 M Ammonium Sulphate, 0.1 M Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.31 Å R-free 0.221
5AN3 Structure of an Sgt1-Skp1 Complex Deposited 2015-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–35（35 aa） Fragment：BTBPOZ DOMAIN, UNP RESIDUES 1-35,65-158 Chain D 65–158（94 aa） Fragment：BTBPOZ DOMAIN, UNP RESIDUES 1-35,65-158	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.325 M MGCL2, 22.5% PEG-6000, 0.1 M TRIS-HCL PH 8	Resolution 2.82 Å R-free 0.241
6F07 CBF3 Core Complex Deposited 2017-11-17	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–194（194 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6FE8 Cryo-EM structure of the core Centromere Binding Factor 3 complex Deposited 2017-12-30	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 2–194（193 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6GSA Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10 Deposited 2018-06-13	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: tetrameric	Chain C 2–194（193 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6GYP Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore Deposited 2018-07-01	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–194（194 aa）	Not recorded	MET METHIONINE × 1 PHE PHENYLALANINE × 1 ASN ASPARAGINE × 1 ARG ARGININE × 1 THR THREONINE × 2 GLN GLUTAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6GYS Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore Deposited 2018-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain D 1–194（194 aa） Chain K 1–194（194 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
7K79 CBF3 Deposited 2020-09-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain N 1–194（194 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7PMN S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation II) Deposited 2021-09-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain K 1–194（194 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Manual plunger	Resolution 3.20 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric	Chain SK 1–194（194 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
9COP Yeast RAVE bound to V-ATPase V1 complex Deposited 2024-07-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain z 1–194（194 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

13 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SKP1_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–194； UniProt 1–194

Centromere DNA-binding protein complex CBF3 subunit A

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P32504

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 E； UniProt 1–956	Not recorded	Centromere DNA-binding protein complex CBF3 subunit B × 1 （P40969） Centromere DNA-binding protein complex CBF3 subunit C × 1 （P35203） Centromere DNA-binding protein complex CBF3 subunit B × 1 （P40969） Suppressor of kinetochore protein 1 × 1 （P52286） ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

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 6GYU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4ACO Structure of the budding yeast Ndc10 N-terminal domain Deposited 2011-12-16	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–956（956 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.89 Å R-free 0.232
6GSA Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10 Deposited 2018-06-13	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: tetrameric	Chain E 2–553（552 aa） Fragment：UNP residues 2-553	Mutation：Construct comprising residues 1-554 with C-terminal Strep tag	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6GYP Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore Deposited 2018-07-01	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–956（956 aa）	Not recorded	MET METHIONINE × 1 PHE PHENYLALANINE × 1 ASN ASPARAGINE × 1 ARG ARGININE × 1 THR THREONINE × 2 GLN GLUTAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6GYS Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore Deposited 2018-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain E 1–956（956 aa） Chain L 1–956（956 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å

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

View Construct and Data Evidence

UniProt name	CBF3A_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–956； UniProt 1–956

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	6gyu
Deposition date deposition_date	2018-07-02
Structure title title	Cryo-EM structure of the CBF3-msk complex of the budding yeast kinetochore
Keywords keywords	Complex, DNA binding protein; DNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	49.08 Å
Radius of gyration Rg (electron density) rg_electron	49.09 Å
Forward intensity I(0) i0	887694000.00
Molecular weight molecular_weight	257220.0 kDa
Excluded volume excluded_volume	325780 Å³
Envelope volume envelope_volume	450710 Å³
Hydration-shell volume shell_volume	79030 Å³
Envelope diameter envelope_diameter	169.1 Å
Shell Rg shell_rg	51.34 Å
Envelope Rg envelope_rg	48.14 Å
Shape Rg shape_rg	49.13 Å
Total Rg total_rg	49.05 Å
Total atoms total_atoms	18159
Residues n_residues	2193
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	169.2 Å
Rg (real space) rg_real	49.41 Å
Rg uncertainty (real space) rg_real_error	1.58 Å
I(0) (real space) i0_real	8.8770e+08
I(0) uncertainty (real space) i0_real_error	1.9000e+07
Rg (reciprocal space) rg_reciprocal	49.08 Å
I(0) (reciprocal space) i0_reciprocal	887300000.0000
Solution quality estimate total_estimate	0.8466
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.6 Å
Skewness Skewness skewness	0.472
Kurtosis Kurtosis kurtosis	-0.360
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	149300000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.640

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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	Centromere DNA-binding protein complex CBF3 subunit B
Molecular weight formula_weight	71439.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	18159

MFNRTTQLKSKHPCSVCTRRKVKCDRMIPCGNCRKRGQDSECMKSTKLITASSSKEYLPDLLLFWQNYEYWITNIGLYKTKQRDLTRTPANLDTDTEECMFWMNYLQKDQSFQLMNFAMENLGALYFGSIGDISELYLRVEQYWDRRADKNHSVDGKYWDALIWSVFTMCIYYMPVEKLAEIFSVYPLHEYLGSNKRLNWEDGMQLVMCQNFARCSLFQLKQCDFMAHPDIRLVQAYLILATTTFPYDEPLLANSLLTQCIHTFKNFHVDDFRPLLNDDPVESIAKVTLGRIFYRLCGCDYLQSGPRKPIALHTEVSSLLQHAAYLQDLPNVDVYREENSTEVLYWKIISLDRDLDQYLNKSSKPPLKTLDAIRRELDIFQYKVDSLEEDFRSNNSRFQKFIALFQISTVSWKLFKMYLIYYDTADSLLKVIHYSKVIISLIVNNFHAKSEFFNRHPMVMQTITRVVSFISFYQIFVESAAVKQLLVDLTELTANLPTIFGSKLDKLVYLTERLSKLKLLWDKVQLLDSGDSFYHPVFKILQNDIKIIELKNDEMFSLIKGLGSLVPLNKLRQESLLEEEDENNTEPSDFRTIVEEFQSEYNISDILS

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	unidentified baculovirus

Entity 2 Entity 2 polymer

Description description	Centromere DNA-binding protein complex CBF3 subunit C
Molecular weight formula_weight	56416.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MPSFNPVRFLELPIDIRKEVYFHLDGNFCGAHPYPIDILYKSNDVELPGKPSYKRSKRSKKLLRYMYPVFATYLNIFEYSPQLIEKWLEYAFWLRYDCLVLDCFKVNHLYDGTLIDALEWTYLDNELRLAYFNKASMLEVWYTFKEYKKWVIDSVAFDELDLLNVSNIQFNIDNLTPQLVDKCLSILEQKDLFATIGEVQFGQDEEVGEEKDVDVSGANSDENSSPSSTIKNKKRSASKRSHSDNGNVGATHNQLTSISVIRTIRSMESMKSLRKITVRGEKLYELLINFHGFRDNPGKTISYIVKRRINEIRLSRMNQISRTGLADFTRWDNLQKLVLSRVAYIDLNSIVFPKNFKSLTMKRVSKIKWWNIEENILKELKVDKRTFKSLYIKEDDSKFTKFFNLRHTRIKELDKSEINQITYLRCQAIVWLSFRTLNHIKLQNVSEVFNNIIVPRALFDSKRVEIYRCEKISQVLVI

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	unidentified baculovirus

Entity 3 Entity 3 polymer

Description description	Centromere DNA-binding protein complex CBF3 subunit B
Molecular weight formula_weight	66401.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MFNRITASSSKEYLPDLLLFWQNYEYWITNIGLYKTKQRDLTRTPANLDTDTEECMFWMNYLQKDQSFQLMNFAMENLGALYFGSIGDISELYLRVEQYWDRRADKNHSVDGKYWDALIWSVFTMCIYYMPVEKLAEIFSVYPLHEYLGSNKRLNWEDGMQLVMCQNFARCSLFQLKQCDFMAHPDIRLVQAYLILATTTFPYDEPLLANSLLTQCIHTFKNFHVDDFRPLLNDDPVESIAKVTLGRIFYRLCGCDYLQSGPRKPIALHTEVSSLLQHAAYLQDLPNVDVYREENSTEVLYWKIISLDRDLDQYLNKSSKPPLKTLDAIRRELDIFQYKVDSLEEDFRSNNSRFQKFIALFQISTVSWKLFKMYLIYYDTADSLLKVIHYSKVIISLIVNNFHAKSEFFNRHPMVMQTITRVVSFISFYQIFVESAAVKQLLVDLTELTANLPTIFGSKLDKLVYLTERLSKLKLLWDKVQLLDSGDSFYHPVFKILQNDIKIIELKNDEMFSLIKGLGSLVPLNKLRQESLLEEEDENNTEPSDFRTIVEEFQSEYNISDILS

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	unidentified baculovirus

Entity 4 Entity 4 polymer

Description description	Suppressor of kinetochore protein 1
Molecular weight formula_weight	22357.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSKDNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWDREFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEEEAAIRRENEWAEDR

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	unidentified baculovirus

Entity 5 Entity 5 polymer

Description description	Centromere DNA-binding protein complex CBF3 subunit A
Molecular weight formula_weight	112066.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MRSSILFLLKLMKIMDVQQQQEAMSSEDRFQELVDSLKPRTAHQYKTYYTKYIQWCQLNQIIPTPEDNSVNSVPYKDLPISAELIHWFLLDTLITDDKPGEKREETEDLDEEEENSFKIATLKKIIGSLNFLSKLCKVHENPNANIDTKYLESVTKLHTHWIDSQKAITTNETNNTNTQVLCPPLLKVSLNLWNPETNHLSEKFFKTCSEKLRFLVDFQLRSYLNLSFEERSKIRFGSLKLGKRDRDAIIYHKVTHSAEKKDTPGHHQLLALLPQDCPFICPQTTLAAYLYLRFYGIPSVSKGDGFPNLNADENGSLLQDIPILRGKSLTTYPREETFSNYYTTVFRYCHLPYKRREYFNKCNLVYPTWDEDTFRTFFNEENHGNWLEQPEAFAFPDKIPFDFKKIMNFKSPYTSYSTNAKKDPFPPPKDLLVQIFPEIDEYKRHDYEGLSQNSRDFLDLMEVLRERFLSNLPWIYKFFPNHDIFQDPIFGNSDFQSYFNDKTIHSKGSPILSFDILPGFNKIYKNKTNFYSLLIERPSQLTFASSHNPDTHPTQKQESEGPLQMSQLDTTQLNELLKQQSFEYVQFQTLSNFQILLSVFNKIFEKLEMKKSSRGYILHQLNLFKITLDERIKKSKIDDADKFIRDNQPIKKEENIVNEDGPNTSRRTKRPKQIRLLSIADSSDESSTEDSNVFKKDGESIEDGAYGENEDENDSEMQEQLKSMINELINSKISTFLRDQMDQFELKINALLDKILEEKVTRIIEQKLGSHTGKFSTLKRPQLYMTEEHNVGFDMEVPKKLRTSGKYAETVKDNDDHQAMSTTASPSPEQDQEAKSYTDEQEFMLDKSIDSIEGIILEWFTPNAKYANQCVHSMNKSGNKSWRANCEALYKERKSIVEFYIYLVNHESLDRYKAVDICEKLRDQNEGSFSRLAKFLRKWRHDHQNSFDGLLVYLSN

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	unidentified baculovirus

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6gyuD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	6gyuE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	443 — hpI Integrase; Chain A
Homologous superfamily homologous superfamily	20 — Centromere DNA-binding protein complex CBF3 subunit, domain 2

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8. Citations (1)

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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	1

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

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	198010

fit	/app/data/saxs_computation/gy/6gyu/6gyu.fit
pddf	/app/data/pr_computation/gy/6gyu/6gyu.pr.out
profile	/app/data/saxs_computation/gy/6gyu/6gyu.dat

Cryo-EM structure of the CBF3-msk complex of the budding yeast kinetochore

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

Centromere DNA-binding protein complex CBF3 subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Centromere DNA-binding protein complex CBF3 subunit C

State in the Current Structure

Other States of the Same Protein in the Database

Suppressor of kinetochore protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Centromere DNA-binding protein complex CBF3 subunit A

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

冷冻电镜 EM 3D

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 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)