SAXSdb — 4geq

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

Kinetochore protein SPC25

Saccharomyces cerevisiae 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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 133–221	Fragment：Spc25p C-terminal domain, residues 133-221	Kinetochore protein SPC24 × 1 （Q04477） Kinetochore-associated protein CNN1 × 1 （P43618） 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 133–221	Fragment：Spc25p C-terminal domain, residues 133-221	Kinetochore protein SPC24 × 1 （Q04477） Kinetochore-associated protein CNN1 × 1 （P43618） 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

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 4GEQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2FTX Crystal structure of the yeast kinetochore Spc24/Spc25 globular domain Deposited 2006-01-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 133–221（89 aa） Fragment：Spc25p globular domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 10.5；293 K；0.1 M CAPS, pH 10.5, 1.2 M NaH2PO4/0.8 M K2HPO4, 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 10.50	Resolution 1.90 Å R-free 0.226
2FV4 NMR solution structure of the yeast kinetochore Spc24/Spc25 globular domain Deposited 2006-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 128–221（94 aa） Fragment：SPC25P GLOBULAR DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate buffer；Pressure ambient NMR sample composition 1.5 mM spc25G U-15N,13C,85%-2H, 1.5 mM spc24G natural abundance isotopes, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C,85%-2H, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G U-15N,13C, 1.5 mM spc24G natural abundance isotopes, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G U-15N,13C, 85%-2H, 1.5 mM spc24G natural abundance isotopes, 50 mg/mL Pf1 phage, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C, 50 mg/mL Pf1 phage, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O.	Resolution not provided
5T6J Structure of the MIND Complex Shows a Regulatory Focus of Yeast Kinetochore Assembly Deposited 2016-09-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 133–221（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M HEPES, pH 7.0-7.5, 1.0 M potassium sodium tartrate, 0.2 M lithium sulfate	Resolution 1.75 Å R-free 0.242
5TCS Crystal structure of a Dwarf Ndc80 Tetramer Deposited 2016-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–31（31 aa） Chain D 138–221（84 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；1.2 magnesium sulfate, 0.1 M ME pH 6.0	Resolution 2.83 Å R-free 0.266
5TD8 Crystal structure of an Extended Dwarf Ndc80 Complex Deposited 2016-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–45（45 aa） Chain D 138–221（84 aa）	Not recorded	HG MERCURY (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG 4,000, 0.1 M CHES, pH 9.0	Resolution 7.53 Å R-free 0.328
8V10 Structure of a Saccharomyces cerevisiae Mps1 peptide bound to dwarf Ndc80 Complex Deposited 2023-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–31（31 aa） Chain D 138–221（84 aa）	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；13% polyethylene glycol 8000, 1M sodium chloride 100 mM PIPES pH 6.1	Resolution 3.02 Å R-free 0.271
8V11 Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex Deposited 2023-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–31（31 aa） Chain D 138–220（83 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291.15 K；15% polyethylene glycol 2000 monomethyl ether,500 mM sodium chloride,50 mM Tris pH 7.5	Resolution 3.95 Å R-free 0.327
8V11 Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex Deposited 2023-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 1–31（31 aa） Chain H 138–220（83 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291.15 K；15% polyethylene glycol 2000 monomethyl ether,500 mM sodium chloride,50 mM Tris pH 7.5	Resolution 3.95 Å R-free 0.327
9S4Q Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex lacking the Mis12c(Mtw1c) head 2 domain Deposited 2025-07-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain 25 1–221（221 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å
9S5N Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex containing the Mis12c(Mtw1c) head 2 domain Deposited 2025-07-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain 25 1–221（221 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.20 Å

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

View Construct and Data Evidence

UniProt name	SPC25_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–90； UniProt 133–221 Author chain C； PDBConstruct 2–90； UniProt 133–221

Kinetochore protein SPC24

Saccharomyces cerevisiae S288c

UniProt Q04477

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 155–213	Fragment：Spc24p C-terminal domain, residues 155-213	Kinetochore protein SPC25 × 1 （P40014） Kinetochore-associated protein CNN1 × 1 （P43618） 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 155–213	Fragment：Spc24p C-terminal domain, residues 155-213	Kinetochore protein SPC25 × 1 （P40014） Kinetochore-associated protein CNN1 × 1 （P43618） 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

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 4GEQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2FTX Crystal structure of the yeast kinetochore Spc24/Spc25 globular domain Deposited 2006-01-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 154–213（60 aa） Fragment：Spc24p globular domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 10.5；293 K；0.1 M CAPS, pH 10.5, 1.2 M NaH2PO4/0.8 M K2HPO4, 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 10.50	Resolution 1.90 Å R-free 0.226
2FV4 NMR solution structure of the yeast kinetochore Spc24/Spc25 globular domain Deposited 2006-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 138–213（76 aa） Fragment：SPC24P GLOBULAR DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate buffer；Pressure ambient NMR sample composition 1.5 mM spc25G U-15N,13C,85%-2H, 1.5 mM spc24G natural abundance isotopes, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C,85%-2H, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G U-15N,13C, 1.5 mM spc24G natural abundance isotopes, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G U-15N,13C, 85%-2H, 1.5 mM spc24G natural abundance isotopes, 50 mg/mL Pf1 phage, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C, 50 mg/mL Pf1 phage, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O.	Resolution not provided
5T6J Structure of the MIND Complex Shows a Regulatory Focus of Yeast Kinetochore Assembly Deposited 2016-09-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 155–213（59 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M HEPES, pH 7.0-7.5, 1.0 M potassium sodium tartrate, 0.2 M lithium sulfate	Resolution 1.75 Å R-free 0.242
5TCS Crystal structure of a Dwarf Ndc80 Tetramer Deposited 2016-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–48（48 aa） Chain C 162–213（52 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；1.2 magnesium sulfate, 0.1 M ME pH 6.0	Resolution 2.83 Å R-free 0.266
5TD8 Crystal structure of an Extended Dwarf Ndc80 Complex Deposited 2016-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–62（62 aa） Chain C 162–213（52 aa）	Not recorded	HG MERCURY (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG 4,000, 0.1 M CHES, pH 9.0	Resolution 7.53 Å R-free 0.328
8V10 Structure of a Saccharomyces cerevisiae Mps1 peptide bound to dwarf Ndc80 Complex Deposited 2023-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–48（48 aa） Chain C 162–213（52 aa）	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；13% polyethylene glycol 8000, 1M sodium chloride 100 mM PIPES pH 6.1	Resolution 3.02 Å R-free 0.271
8V11 Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex Deposited 2023-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–48（48 aa） Chain C 162–212（51 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291.15 K；15% polyethylene glycol 2000 monomethyl ether,500 mM sodium chloride,50 mM Tris pH 7.5	Resolution 3.95 Å R-free 0.327
8V11 Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex Deposited 2023-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 1–48（48 aa） Chain G 162–212（51 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291.15 K；15% polyethylene glycol 2000 monomethyl ether,500 mM sodium chloride,50 mM Tris pH 7.5	Resolution 3.95 Å R-free 0.327
9S4Q Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex lacking the Mis12c(Mtw1c) head 2 domain Deposited 2025-07-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain 24 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å
9S5N Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex containing the Mis12c(Mtw1c) head 2 domain Deposited 2025-07-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain 24 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.20 Å

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

View Construct and Data Evidence

UniProt name	SPC24_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–60； UniProt 155–213 Author chain D； PDBConstruct 2–60； UniProt 155–213

Kinetochore-associated protein CNN1

OrganismNot specified

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 60–84	Fragment：Cnn1p N-terminal motif, residues 60-84	Kinetochore protein SPC25 × 1 （P40014） Kinetochore protein SPC24 × 1 （Q04477） 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 60–84	Fragment：Cnn1p N-terminal motif, residues 60-84	Kinetochore protein SPC25 × 1 （P40014） Kinetochore protein SPC24 × 1 （Q04477） 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

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 4GEQ	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 construct Different oligomeric state Different ligand/ion 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
6YPC Crystal structure of the kinetochore subunits H/I/K/T/W penta-complex from S. cerevisiae at 2.9 angstroms Deposited 2020-04-15	Different construct Different oligomeric state Different ligand/ion 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	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
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26	Different construct Different oligomeric state Different ligand/ion 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 construct Different oligomeric state Different ligand/ion 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 ligand/ion 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 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CNN1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–25； UniProt 60–84 Author chain F； PDBConstruct 1–25； UniProt 60–84

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	4geq
Deposition date deposition_date	2012-08-02
Structure title title	Crystal structure of the Spc24-Spc25/Cnn1 binding interface
Keywords keywords	protein-protein complex, Ndc80-binding motif, RWD domain, kinetochore components, nucleus, 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	23.19 Å
Radius of gyration Rg (electron density) rg_electron	21.97 Å
Forward intensity I(0) i0	23064300.00
Molecular weight molecular_weight	36778.0 kDa
Excluded volume excluded_volume	46202 Å³
Envelope volume envelope_volume	57182 Å³
Hydration-shell volume shell_volume	22025 Å³
Envelope diameter envelope_diameter	71.8 Å
Shell Rg shell_rg	28.23 Å
Envelope Rg envelope_rg	21.81 Å
Shape Rg shape_rg	21.97 Å
Total Rg total_rg	22.79 Å
Total atoms total_atoms	2594
Residues n_residues	331
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	71.9 Å
Rg (real space) rg_real	23.12 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	2.3060e+07
I(0) uncertainty (real space) i0_real_error	2.9940e+05
Rg (reciprocal space) rg_reciprocal	23.14 Å
I(0) (reciprocal space) i0_reciprocal	23060000.0000
Solution quality estimate total_estimate	0.9109
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.7 Å
Skewness Skewness skewness	0.222
Kurtosis Kurtosis kurtosis	-0.510
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3580000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Kinetochore protein SPC25
Molecular weight formula_weight	9889.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2750

MNDAAEVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288c
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Kinetochore protein SPC24
Molecular weight formula_weight	7903.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MANENILKLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGKHHHHHH

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288c
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Kinetochore-associated protein CNN1
Molecular weight formula_weight	2848.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

NKDPNEVRSFLQDLSQVLARKSQGN

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	150

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4geqA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	457 — Copper Amine Oxidase; Chain A, domain 1
Homologous superfamily homologous superfamily	50 — Chromosome segregation protein Spc25

Domain ID domain_id	4geqB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	430 —

Domain ID domain_id	4geqC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	457 — Copper Amine Oxidase; Chain A, domain 1
Homologous superfamily homologous superfamily	50 — Chromosome segregation protein Spc25

Domain ID domain_id	4geqD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	430 —

▶

8. Citations (1)

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Unit-cell length a length_a	34.142 Å
Unit-cell length b length_b	61.848 Å
Unit-cell length c length_c	139.056 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	37.090 Å
R factor r_factor	0.2092
R_work r_work	0.2067
R_free r_free	0.2580

fit	/app/data/saxs_computation/ge/4geq/4geq.fit
pddf	/app/data/pr_computation/ge/4geq/4geq.pr.out
profile	/app/data/saxs_computation/ge/4geq/4geq.dat

Crystal structure of the Spc24-Spc25/Cnn1 binding interface

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

Kinetochore protein SPC25

State in the Current Structure

Other States of the Same Protein in the Database

Kinetochore protein SPC24

State in the Current Structure

Other States of the Same Protein in the Database

Kinetochore-associated protein CNN1

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 (5)

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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)