2vfx

Structure of the Symmetric Mad2 Dimer

Method: X-RAY DIFFRACTION D_max: 183.0 Å Quality: GOOD

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

MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A

HOMO SAPIENS

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–205	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 3 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
10	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain J； UniProt 1–205	Mutation：YES	CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
11	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain K； UniProt 1–205	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 2 PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
12	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain L； UniProt 1–205	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 3 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–205	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 4 PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–205	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 3 PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–205	Mutation：YES	CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 1–205	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 5 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 1–205	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 2 PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 1–205	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain H； UniProt 1–205	Mutation：YES	PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
9	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain I； UniProt 1–205	Mutation：YES	CL CHLORIDE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247

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 2VFX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DUJ SOLUTION STRUCTURE OF THE SPINDLE ASSEMBLY CHECKPOINT PROTEIN HUMAN MAD2 Deposited 2000-01-17	Different construct Different mutation/modification 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 11–195（185 aa） Fragment：FULL PROTEIN WITHOUT BOTH N- AND C-TERMINAL 10 RESIDUES	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 300mM KCl；Pressure ambient NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 300mM KCl；Pressure ambient NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 300mM KCl；Pressure ambient NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 300mM KCl；Pressure ambient NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 300mM KCl；Pressure ambient NMR sample composition 1.2mM Mad2 protein U-15N,13C,2H; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.4mM Mad2 protein U-15N,13C; U-60% 2H; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.5mM Mad2 protein U-15N; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.6mM Mad2 protein U-10% 13C; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 100% D2O \| 100% D2O NMR sample composition 1.7mM Mad2 protein U-15N,13C; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 100% D2O \| 100% D2O	Resolution not provided
1GO4 Crystal structure of Mad1-Mad2 reveals a conserved Mad2 binding motif in Mad1 and Cdc20. Deposited 2001-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–205（205 aa） Chain B 1–205（205 aa） Chain C 1–205（205 aa） Chain D 1–205（205 aa）	Mutation：R133A Mutation：R133A Mutation：R133A Mutation：R133A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；PROTEIN CONCENTRATION 7.5 MG/ML HANGING DROP METHOD, WELL=100 MM AMMONIUM SULPHATE, 100 MM AMMONIUM CITRATE PH 5.2, 10 MM DTT	Resolution 2.05 Å R-free 0.268
1KLQ The Mad2 Spindle Checkpoint Protein Undergoes Similar Major Conformational Changes upon Binding to Either Mad1 or Cdc20 Deposited 2001-12-12	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 × 2 PDB declaration: dimeric	Chain A 9–205（197 aa） Fragment：MISSING N-TERMINAL 10 RESIDUES	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0.3M KCl；Pressure ambient NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0.3M KCl；Pressure ambient NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0.3M KCl；Pressure ambient NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0.3M KCl；Pressure ambient NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0.3M KCl；Pressure ambient NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0.3M KCl；Pressure ambient NMR sample composition 0.8mM Mad2 protein U-15N; 1mM MBP1 NA; 50mM phosphate buffer; 0.3M KCl; 1mM DTT \| 90% H2O/10% D2O NMR sample composition 0.8mM Mad2 protein U-15N, 13C, 2H; 1mM MBP1 NA; 50mM phosphate buffer; 0.3M KCl; 1mM DTT \| 90% H2O/10% D2O NMR sample composition 0.8mM Mad2 protein U-15N, 13C; 1mM MBP1 NA; 50mM phosphate buffer; 0.3M KCl; 1mM DTT \| 90% H2O/10% D2O NMR sample composition 0.8mM Mad2 protein U-15N, 13C, U-60% 2H; 1mM MBP1 NA; 50mM phosphate buffer; 0.3M KCl; 1mM DTT \| 90% H2O/10% D2O NMR sample composition 0.8mM MBP1 U-15N; 1mM Mad2 protein NA; 50mM phosphate buffer; 0.3M KCl; 1mM DTT \| 90% H2O/10% D2O NMR sample composition 0.8mM MBP1 U-15N, 13C; 1mM Mad2 protein NA; 50mM phosphate buffer; 0.3M KCl; 1mM DTT \| 90% H2O/10% D2O	Resolution not provided
1S2H The Mad2 spindle checkpoint protein possesses two distinct natively folded states Deposited 2004-01-08	Different mutation/modification 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 1–205（205 aa）	Mutation：R133A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 0.3M KCl；Pressure ambient NMR sample composition 0.8mM Mad2 protein U-15N,13C,2H \| 90% H2O, 10% D2O; 50mM phosphate buffer; 0.3M KCl; 1mM DTT NMR sample composition 0.8mM Mad2 protein U-15N \| 90% H2O, 10% D2O; 50mM phosphate buffer; 0.3M KCl; 1mM DTT NMR sample composition 0.8mM Mad2 protein U-15N,13C \| 90% H2O, 10% D2O; 50mM phosphate buffer; 0.3M KCl; 1mM DTT	Resolution not provided
2QYF Crystal structure of the Mad2/p31(comet)/Mad2-binding peptide ternary complex Deposited 2007-08-14	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 1–205（205 aa）	Mutation：L13A 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 5；289 K；16% (w/v) PEG 3350, 16% (v/v) glycerol, 125 mM sodium phosphate (pH 5.0), 100 mM NaCl, 25 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.257
2QYF Crystal structure of the Mad2/p31(comet)/Mad2-binding peptide ternary complex Deposited 2007-08-14	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 1–205（205 aa）	Mutation：L13A 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 5；289 K；16% (w/v) PEG 3350, 16% (v/v) glycerol, 125 mM sodium phosphate (pH 5.0), 100 mM NaCl, 25 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.257
2V64 Crystallographic structure of the conformational dimer of the Spindle Assembly Checkpoint protein Mad2. Deposited 2007-07-13	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 2–205（204 aa） Fragment：RESIDUES 2-205 Chain E 2–108（107 aa） Fragment：RESIDUES 2-108,118-205 Chain E 118–205（88 aa） Fragment：RESIDUES 2-108,118-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1M NAACETATE PH 4.6, 3.5M NAFORMATE	Resolution 2.90 Å R-free 0.273
2V64 Crystallographic structure of the conformational dimer of the Spindle Assembly Checkpoint protein Mad2. Deposited 2007-07-13	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 2–205（204 aa） Fragment：RESIDUES 2-205 Chain D 2–108（107 aa） Fragment：RESIDUES 2-108,118-205 Chain D 118–205（88 aa） Fragment：RESIDUES 2-108,118-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1M NAACETATE PH 4.6, 3.5M NAFORMATE	Resolution 2.90 Å R-free 0.273
2V64 Crystallographic structure of the conformational dimer of the Spindle Assembly Checkpoint protein Mad2. Deposited 2007-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 2–205（204 aa） Fragment：RESIDUES 2-205 Chain H 2–108（107 aa） Fragment：RESIDUES 2-108,118-205 Chain H 118–205（88 aa） Fragment：RESIDUES 2-108,118-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1M NAACETATE PH 4.6, 3.5M NAFORMATE	Resolution 2.90 Å R-free 0.273
3GMH Crystal Structure of the Mad2 Dimer Deposited 2009-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 11–205（195 aa） Chain B 11–205（195 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；1.6M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.95 Å R-free 0.251
3GMH Crystal Structure of the Mad2 Dimer Deposited 2009-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 11–205（195 aa） Chain D 11–205（195 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；1.6M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.95 Å R-free 0.251
3GMH Crystal Structure of the Mad2 Dimer Deposited 2009-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 11–205（195 aa） Chain F 11–205（195 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；1.6M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.95 Å R-free 0.251
3GMH Crystal Structure of the Mad2 Dimer Deposited 2009-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 11–205（195 aa） Chain H 11–205（195 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；1.6M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.95 Å R-free 0.251
3GMH Crystal Structure of the Mad2 Dimer Deposited 2009-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 11–205（195 aa） Chain J 11–205（195 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；1.6M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.95 Å R-free 0.251
3GMH Crystal Structure of the Mad2 Dimer Deposited 2009-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain K 11–205（195 aa） Chain L 11–205（195 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；1.6M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.95 Å R-free 0.251
5KHU Model of human Anaphase-promoting complex/Cyclosome (APC15 deletion mutant), in complex with the Mitotic checkpoint complex (APC/C-CDC20-MCC) based on cryo EM data at 4.8 Angstrom resolution Deposited 2016-06-15	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 × 23 PDB declaration: 23-meric	Chain T 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
5LCW Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Mitotic checkpoint complex (APC/C-MCC) at 4.2 angstrom resolution Deposited 2016-06-22	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 × 23 PDB declaration: 23-meric	Chain Z 1–205（205 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
6F0X Cryo-EM structure of TRIP13 in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20 Deposited 2017-11-20	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 × 9 PDB declaration: nonameric	Chain Z 1–205（205 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
6TLJ Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Mitotic checkpoint complex (APC/C-MCC) at 3.8 angstrom resolution Deposited 2019-12-02	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 × 23 PDB declaration: 23-meric	Chain Z 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å

11 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MD2L1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–206； UniProt 1–205 Author chain B； PDBConstruct 2–206； UniProt 1–205 Author chain C； PDBConstruct 2–206； UniProt 1–205 Author chain D； PDBConstruct 2–206； UniProt 1–205 Author chain E； PDBConstruct 2–206； UniProt 1–205 Author chain F； PDBConstruct 2–206； UniProt 1–205 Author chain G； PDBConstruct 2–206； UniProt 1–205 Author chain H； PDBConstruct 2–206； UniProt 1–205 Author chain I； PDBConstruct 2–206； UniProt 1–205 Author chain J； PDBConstruct 2–206； UniProt 1–205 Author chain K； PDBConstruct 2–206； UniProt 1–205 Author chain L； PDBConstruct 2–206； UniProt 1–205

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2vfx
Deposition date deposition_date	2007-11-05
Structure title title	Structure of the Symmetric Mad2 Dimer
Keywords keywords	MAD2, MAD1, CDC2, NUCLEUS, MITOSIS, ANAPHASE, CELL CYCLE, CELL DIVISION, SPINDLE CHECKPOINT, ANAPHASE-PROMOTING COMPLEX; 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	53.98 Å
Radius of gyration Rg (electron density) rg_electron	53.82 Å
Forward intensity I(0) i0	1063130000.00
Molecular weight molecular_weight	281050.0 kDa
Excluded volume excluded_volume	355660 Å³
Envelope volume envelope_volume	572130 Å³
Hydration-shell volume shell_volume	88686 Å³
Envelope diameter envelope_diameter	189.9 Å
Shell Rg shell_rg	56.70 Å
Envelope Rg envelope_rg	52.50 Å
Shape Rg shape_rg	53.81 Å
Total Rg total_rg	53.95 Å
Total atoms total_atoms	19764
Residues n_residues	2438
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	183.0 Å
Rg (real space) rg_real	53.99 Å
Rg uncertainty (real space) rg_real_error	1.89 Å
I(0) (real space) i0_real	1.0630e+09
I(0) uncertainty (real space) i0_real_error	2.3030e+07
Rg (reciprocal space) rg_reciprocal	53.96 Å
I(0) (reciprocal space) i0_reciprocal	1063000000.0000
Solution quality estimate total_estimate	0.8870
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	63.1 Å
Skewness Skewness skewness	0.294
Kurtosis Kurtosis kurtosis	-0.505
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	73090000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.888

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A
Molecular weight formula_weight	23516.7 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	21651

GMALQLSREQGITARGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQLKDWLYKSSVQKLVVVISNIESGEVLERWQFDIESDKTAKDDSAPREKSQKAIQDEIRSVIRQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSEEVRLRSFTTTIHKVNSMVAYKIPVND

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	37

Entity 4 Entity 4 non-polymer

Description description	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
Molecular weight formula_weight	354.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
Molecular weight formula_weight	634.8 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1591

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2vfxa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

Domain ID domain_id	d2vfxb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

Domain ID domain_id	d2vfxc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

Domain ID domain_id	d2vfxd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

Domain ID domain_id	d2vfxe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

Domain ID domain_id	d2vfxf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

Domain ID domain_id	d2vfxg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

Domain ID domain_id	d2vfxh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

Domain ID domain_id	d2vfxi_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

Domain ID domain_id	d2vfxj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

Domain ID domain_id	d2vfxk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

Domain ID domain_id	d2vfxl_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

CATH v4.4 (12 domains)

Domain ID domain_id	2vfxA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2vfxB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2vfxC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2vfxD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2vfxE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2vfxF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2vfxG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2vfxH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2vfxI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2vfxJ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2vfxK00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2vfxL00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

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8. Citations (1)

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Unit-cell length a length_a	109.337 Å
Unit-cell length b length_b	191.407 Å
Unit-cell length c length_c	154.307 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	0.2090
R_work r_work	0.2080
R_free r_free	0.2470

fit	/app/data/saxs_computation/vf/2vfx/2vfx.fit
pddf	/app/data/pr_computation/vf/2vfx/2vfx.pr.out
profile	/app/data/saxs_computation/vf/2vfx/2vfx.dat