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3gmh

Crystal Structure of the Mad2 Dimer

Method: X-RAY DIFFRACTION Dmax: 160.8 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

UniProt Q13257

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 11–205 Chain B； UniProt 11–205 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
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 11–205 Chain D； UniProt 11–205 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
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 11–205 Chain F； UniProt 11–205 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
4 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 11–205 Chain H； UniProt 11–205 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
5 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain I； UniProt 11–205 Chain J； UniProt 11–205 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
6 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain K； UniProt 11–205 Chain L； UniProt 11–205 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

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 3GMH 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–205（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 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 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 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 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
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–205（205 aa）
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
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain J 1–205（205 aa）
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
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 11 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain K 1–205（205 aa）
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
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 12 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain L 1–205（205 aa）
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
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–205（205 aa）
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
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–205（205 aa）
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
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–205（205 aa）
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
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–205（205 aa）
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
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 1–205（205 aa）
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
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 1–205（205 aa）
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
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 1–205（205 aa）
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
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain I 1–205（205 aa）
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
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 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 × 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 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 × 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 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 × 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 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 × 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 25 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 13–207； UniProt 11–205 Author chain B； PDBConstruct 13–207； UniProt 11–205 Author chain C； PDBConstruct 13–207； UniProt 11–205 Author chain D； PDBConstruct 13–207； UniProt 11–205 Author chain E； PDBConstruct 13–207； UniProt 11–205 Author chain F； PDBConstruct 13–207； UniProt 11–205 Author chain G； PDBConstruct 13–207； UniProt 11–205 Author chain H； PDBConstruct 13–207； UniProt 11–205 Author chain I； PDBConstruct 13–207； UniProt 11–205 Author chain J； PDBConstruct 13–207； UniProt 11–205 Author chain K； PDBConstruct 13–207； UniProt 11–205 Author chain L； PDBConstruct 13–207； UniProt 11–205

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

SAXS profile for 3gmh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3gmh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3gmh
Deposition date deposition_date2009-03-13
Structure title titleCrystal Structure of the Mad2 Dimer
Keywords keywordsCELL CYCLE, MITOTIC SPINDLE ASSEMBLY CHECKPOINT, Cell division, Mitosis, Nucleus; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier47.98 Å
Radius of gyration Rg (electron density) rg_electron47.72 Å
Forward intensity I(0) i0893309000.00
Molecular weight molecular_weight259720.0 kDa
Excluded volume excluded_volume330030 ų
Envelope volume envelope_volume471800 ų
Hydration-shell volume shell_volume81699 ų
Envelope diameter envelope_diameter191.1 Å
Shell Rg shell_rg52.38 Å
Envelope Rg envelope_rg47.34 Å
Shape Rg shape_rg47.70 Å
Total Rg total_rg47.97 Å
Total atoms total_atoms18301
Residues n_residues2254
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax160.8 Å
Rg (real space) rg_real48.03 Å
Rg uncertainty (real space) rg_real_error1.57 Å
I(0) (real space) i0_real8.9330e+08
I(0) uncertainty (real space) i0_real_error1.5650e+07
Rg (reciprocal space) rg_reciprocal47.98 Å
I(0) (reciprocal space) i0_reciprocal893200000.0000
Solution quality estimate total_estimate0.8141
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary53.6 Å
Skewness Skewness skewness0.355
Kurtosis Kurtosis kurtosis-0.390
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha104800000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.861; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id3gmhA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily10 — HORMA domain
Domain ID domain_id3gmhB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily10 — HORMA domain
Domain ID domain_id3gmhC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily10 — HORMA domain
Domain ID domain_id3gmhD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily10 — HORMA domain
Domain ID domain_id3gmhE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily10 — HORMA domain
Domain ID domain_id3gmhF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily10 — HORMA domain
Domain ID domain_id3gmhG00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily10 — HORMA domain
Domain ID domain_id3gmhH00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily10 — HORMA domain
Domain ID domain_id3gmhI00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily10 — HORMA domain
Domain ID domain_id3gmhJ00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily10 — HORMA domain
Domain ID domain_id3gmhK00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily10 — HORMA domain
Domain ID domain_id3gmhL00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily10 — HORMA domain
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8. Citations (1)

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9. Files and Curves (10)