SAXSdb — 8v11

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

Kinetochore protein NDC80

Saccharomyces cerevisiae

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 114–318 Chain A； UniProt 621–684	Not recorded	Ipl1/Nuf2 chimera protein × 1 （P33895） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014）	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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 114–318 Chain E； UniProt 621–684	Not recorded	Ipl1/Nuf2 chimera protein × 1 （P33895） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014）	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

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 8V11	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5TCS Crystal structure of a Dwarf Ndc80 Tetramer Deposited 2016-09-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 114–318（205 aa） Chain A 621–689（69 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 114–318（205 aa） Chain A 621–691（71 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
8G0Q Crystal structure of the yeast Ndc80:Nuf2 head region with a bound Dam1 segment Deposited 2023-02-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 106–318（213 aa） Fragment：residues 106-318,residues 621-691 Chain A 621–691（71 aa） Fragment：residues 106-318,residues 621-691	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；12% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.1 M ADA buffer pH 6.8	Resolution 3.22 Å R-free 0.285
8G0Q Crystal structure of the yeast Ndc80:Nuf2 head region with a bound Dam1 segment Deposited 2023-02-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 106–318（213 aa） Fragment：residues 106-318,residues 621-691 Chain C 621–691（71 aa） Fragment：residues 106-318,residues 621-691	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；12% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.1 M ADA buffer pH 6.8	Resolution 3.22 Å R-free 0.285
8Q84 Outer kinetochore Dam1 protomer dimer Ndc80-Nuf2 coiled-coil complex Deposited 2023-08-17	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric	Chain A 1–691（691 aa） Chain F 1–691（691 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8Q85 Outer kinetochore Dam1 protomer monomer Ndc80-Nuf2 coiled-coil complex Deposited 2023-08-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain F 1–691（691 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.97 Å
8QAU Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex Deposited 2023-08-23	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 × 5 PDB declaration: pentameric	Chain A 1–691（691 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
8V10 Structure of a Saccharomyces cerevisiae Mps1 peptide bound to dwarf Ndc80 Complex Deposited 2023-11-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 114–318（205 aa） Chain A 621–691（71 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

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

View Construct and Data Evidence

UniProt name	NDC80_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–208； UniProt 114–318 Author chain A； PDBConstruct 209–272； UniProt 621–684 Author chain E； PDBConstruct 4–208； UniProt 114–318 Author chain E； PDBConstruct 209–272； UniProt 621–684

Ipl1/Nuf2 chimera protein

Saccharomyces cerevisiae

UniProt P33895

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 2–153 Chain B； UniProt 407–451	Not recorded	Kinetochore protein NDC80 × 1 （P40460） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014）	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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain F； UniProt 2–153 Chain F； UniProt 407–451	Not recorded	Kinetochore protein NDC80 × 1 （P40460） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014）	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

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 8V11	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5TCS Crystal structure of a Dwarf Ndc80 Tetramer Deposited 2016-09-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 2–153（152 aa） Chain B 407–451（45 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–153（153 aa） Chain B 407–451（45 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
8G0Q Crystal structure of the yeast Ndc80:Nuf2 head region with a bound Dam1 segment Deposited 2023-02-01	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–153（152 aa） Chain B 407–451（45 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；12% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.1 M ADA buffer pH 6.8	Resolution 3.22 Å R-free 0.285
8G0Q Crystal structure of the yeast Ndc80:Nuf2 head region with a bound Dam1 segment Deposited 2023-02-01	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–153（152 aa） Chain D 407–451（45 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；12% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.1 M ADA buffer pH 6.8	Resolution 3.22 Å R-free 0.285
8Q84 Outer kinetochore Dam1 protomer dimer Ndc80-Nuf2 coiled-coil complex Deposited 2023-08-17	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric	Chain B 1–451（451 aa） Chain G 1–451（451 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8Q85 Outer kinetochore Dam1 protomer monomer Ndc80-Nuf2 coiled-coil complex Deposited 2023-08-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain G 1–451（451 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.97 Å
8QAU Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex Deposited 2023-08-23	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 × 5 PDB declaration: pentameric	Chain B 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
8V10 Structure of a Saccharomyces cerevisiae Mps1 peptide bound to dwarf Ndc80 Complex Deposited 2023-11-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 2–153（152 aa） Chain B 407–451（45 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

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

View Construct and Data Evidence

UniProt name	NUF2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 31–182； UniProt 2–153 Author chain B； PDBConstruct 183–227； UniProt 407–451 Author chain F； PDBConstruct 31–182； UniProt 2–153 Author chain F； PDBConstruct 183–227； UniProt 407–451

Kinetochore protein SPC24

Saccharomyces cerevisiae

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–48 Chain C； UniProt 162–212	Not recorded	Kinetochore protein NDC80 × 1 （P40460） Ipl1/Nuf2 chimera protein × 1 （P33895） Kinetochore protein SPC25 × 1 （P40014）	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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain G； UniProt 1–48 Chain G； UniProt 162–212	Not recorded	Kinetochore protein NDC80 × 1 （P40460） Ipl1/Nuf2 chimera protein × 1 （P33895） Kinetochore protein SPC25 × 1 （P40014）	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

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 8V11	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 mutation/modification Different oligomeric state 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
4GEQ Crystal structure of the Spc24-Spc25/Cnn1 binding interface Deposited 2012-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 155–213（59 aa） Fragment：Spc24p C-terminal domain, residues 155-213	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 155–213（59 aa） Fragment：Spc24p C-terminal domain, residues 155-213	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
5T6J Structure of the MIND Complex Shows a Regulatory Focus of Yeast Kinetochore Assembly Deposited 2016-09-01	Different construct Different mutation/modification Different oligomeric state 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 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 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 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
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–48； UniProt 1–48 Author chain C； PDBConstruct 49–99； UniProt 162–212 Author chain G； PDBConstruct 1–48； UniProt 1–48 Author chain G； PDBConstruct 49–99； UniProt 162–212

Kinetochore protein SPC25

Saccharomyces cerevisiae

UniProt P40014

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 1–31 Chain D； UniProt 138–220	Not recorded	Kinetochore protein NDC80 × 1 （P40460） Ipl1/Nuf2 chimera protein × 1 （P33895） Kinetochore protein SPC24 × 1 （Q04477）	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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain H； UniProt 1–31 Chain H； UniProt 138–220	Not recorded	Kinetochore protein NDC80 × 1 （P40460） Ipl1/Nuf2 chimera protein × 1 （P33895） Kinetochore protein SPC24 × 1 （Q04477）	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

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 8V11	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 mutation/modification Different oligomeric state 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
4GEQ Crystal structure of the Spc24-Spc25/Cnn1 binding interface Deposited 2012-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 133–221（89 aa） Fragment：Spc25p C-terminal domain, residues 133-221	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 133–221（89 aa） Fragment：Spc25p C-terminal domain, residues 133-221	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
5T6J Structure of the MIND Complex Shows a Regulatory Focus of Yeast Kinetochore Assembly Deposited 2016-09-01	Different construct Different mutation/modification Different oligomeric state 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 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 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 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
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–31； UniProt 1–31 Author chain D； PDBConstruct 32–114； UniProt 138–220 Author chain H； PDBConstruct 1–31； UniProt 1–31 Author chain H； PDBConstruct 32–114； UniProt 138–220

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	8v11
Deposition date deposition_date	2023-11-19
Structure title title	Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex
Keywords keywords	Stu2, tension sensing, Ndc80, kinetochore, 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	84.43 Å
Radius of gyration Rg (electron density) rg_electron	87.13 Å
Forward intensity I(0) i0	359974000.00
Molecular weight molecular_weight	159570.0 kDa
Excluded volume excluded_volume	200580 Å³
Envelope volume envelope_volume	359380 Å³
Hydration-shell volume shell_volume	46775 Å³
Envelope diameter envelope_diameter	331.7 Å
Shell Rg shell_rg	51.20 Å
Envelope Rg envelope_rg	90.05 Å
Shape Rg shape_rg	87.17 Å
Total Rg total_rg	85.97 Å
Total atoms total_atoms	11239
Residues n_residues	1371
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	219.6 Å
Rg (real space) rg_real	76.16 Å
Rg uncertainty (real space) rg_real_error	1.59 Å
I(0) (real space) i0_real	3.4430e+08
I(0) uncertainty (real space) i0_real_error	6.8120e+06
Rg (reciprocal space) rg_reciprocal	76.48 Å
I(0) (reciprocal space) i0_reciprocal	352200000.0000
Solution quality estimate total_estimate	0.8076
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.8 Å
Skewness Skewness skewness	0.305
Kurtosis Kurtosis kurtosis	-0.998
Angular range angular_range	— – 0.0900 Å⁻¹
Current regularization parameter α current_alpha	0.1706
Highest regularization parameter α highest_alpha	12120000.0000
Real-space data points n_real_points	19
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.013; Oscil: 0.728; Stabil: 0.987; Sysdev: 1.000; Positv: 1.000; Valcen: 0.477; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Kinetochore protein NDC80
Molecular weight formula_weight	32460.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	11265

SNARDPRPLRDKNFQSAIQEEIYDYLKKNKFDIETNHPISIKFLKQPTQKGFIIIFKWLYLRLDPGYGFTKSIENEIYQILKNLRYPFLESINKSQISAVGGSNWHKFLGMLHWMVRTNIKLDMCLNKVDRSLINQNTQEITILSQPLKTLDEQDQRQERYELMVEKLLIDYFTESYKSFLKLEDNYEPSMQELKLGFEKFVHIINTDVTSTELKLEELKVDLNRKRYKLHQQVIHVIDITSKFKINIQSSLENSENELGNVIEELRNLEFE

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Ipl1/Nuf2 chimera protein
Molecular weight formula_weight	26548.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MTSRINKPWRISHSPNSKIPSPVREKLNRLSRNQDVFPILDLQELVICLQSCDFALATQENISRPTSDYMVTLYKQIIENFMGISVESLLNSSNQETGDGHLQEENENIYLDTLNVLVLNKICFKFFENIGVQDFNMTDLYKPEAQRTQRLLSAVVNYARFREERMFDCNSFILQMESLLGQINKLNDEIKQLQKDFEVEVKEIEAAYSLLSGHINKYMNEMLEYMQ

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Kinetochore protein SPC24
Molecular weight formula_weight	11752.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSQKDNLLDNPVEFLKEVRESFDIQQDVDAMKRIRHDLDVIKEESEARLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLG

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Kinetochore protein SPC25
Molecular weight formula_weight	12709.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MASIDAFSDLERRMDGFQKDVAQVLARQQNHVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLAS

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

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8. Citations (1)

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Unit-cell length a length_a	114.757 Å
Unit-cell length b length_b	114.757 Å
Unit-cell length c length_c	423.841 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	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	tetragonal

Resolution resolution	3.950 Å
Low-resolution limit resolution_low	48.530 Å
R factor r_factor	0.2696
R_work r_work	0.2666
R_free r_free	0.3266

fit	/app/data/saxs_computation/v1/8v11/8v11.fit
pddf	/app/data/pr_computation/v1/8v11/8v11.pr.out
profile	/app/data/saxs_computation/v1/8v11/8v11.dat

Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex

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

Kinetochore protein NDC80

State in the Current Structure

Other States of the Same Protein in the Database

Ipl1/Nuf2 chimera protein

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 protein SPC25

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 (4)

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)