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- PDB-3gmh: Crystal Structure of the Mad2 Dimer -

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Basic information

Entry
Database: PDB / ID: 3gmh
TitleCrystal Structure of the Mad2 Dimer
ComponentsMitotic spindle assembly checkpoint protein MAD2A
KeywordsCELL CYCLE / MITOTIC SPINDLE ASSEMBLY CHECKPOINT / Cell division / Mitosis / Nucleus
Function / homology
Function and homology information


mitotic spindle assembly checkpoint MAD1-MAD2 complex / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of mitotic cell cycle spindle assembly checkpoint / establishment of centrosome localization / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / nuclear pore nuclear basket / negative regulation of ubiquitin protein ligase activity / mitotic spindle assembly checkpoint signaling ...mitotic spindle assembly checkpoint MAD1-MAD2 complex / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of mitotic cell cycle spindle assembly checkpoint / establishment of centrosome localization / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / nuclear pore nuclear basket / negative regulation of ubiquitin protein ligase activity / mitotic spindle assembly checkpoint signaling / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / negative regulation of mitotic cell cycle / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / APC-Cdc20 mediated degradation of Nek2A / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / negative regulation of protein catabolic process / mitotic spindle / kinetochore / spindle pole / Separation of Sister Chromatids / cell division / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Mitotic spindle assembly checkpoint protein MAD2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.95 Å
AuthorsOzkan, E. / Luo, X. / Machius, M. / Yu, H. / Deisenhofer, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of an intermediate conformer of the spindle checkpoint protein Mad2.
Authors: Hara, M. / Ozkan, E. / Sun, H. / Yu, H. / Luo, X.
History
DepositionMar 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 2, 2015Group: Database references
Revision 1.3Oct 7, 2015Group: Database references
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitotic spindle assembly checkpoint protein MAD2A
B: Mitotic spindle assembly checkpoint protein MAD2A
C: Mitotic spindle assembly checkpoint protein MAD2A
D: Mitotic spindle assembly checkpoint protein MAD2A
E: Mitotic spindle assembly checkpoint protein MAD2A
F: Mitotic spindle assembly checkpoint protein MAD2A
G: Mitotic spindle assembly checkpoint protein MAD2A
H: Mitotic spindle assembly checkpoint protein MAD2A
I: Mitotic spindle assembly checkpoint protein MAD2A
J: Mitotic spindle assembly checkpoint protein MAD2A
K: Mitotic spindle assembly checkpoint protein MAD2A
L: Mitotic spindle assembly checkpoint protein MAD2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,04224
Polymers285,89012
Non-polymers1,15312
Water0
1
A: Mitotic spindle assembly checkpoint protein MAD2A
B: Mitotic spindle assembly checkpoint protein MAD2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9365
Polymers47,6482
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-48 kcal/mol
Surface area19180 Å2
MethodPISA
2
C: Mitotic spindle assembly checkpoint protein MAD2A
D: Mitotic spindle assembly checkpoint protein MAD2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9365
Polymers47,6482
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-46 kcal/mol
Surface area19790 Å2
MethodPISA
3
E: Mitotic spindle assembly checkpoint protein MAD2A
F: Mitotic spindle assembly checkpoint protein MAD2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7443
Polymers47,6482
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-22 kcal/mol
Surface area19060 Å2
MethodPISA
4
G: Mitotic spindle assembly checkpoint protein MAD2A
H: Mitotic spindle assembly checkpoint protein MAD2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8404
Polymers47,6482
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-33 kcal/mol
Surface area19230 Å2
MethodPISA
5
I: Mitotic spindle assembly checkpoint protein MAD2A
J: Mitotic spindle assembly checkpoint protein MAD2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7443
Polymers47,6482
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-23 kcal/mol
Surface area19030 Å2
MethodPISA
6
K: Mitotic spindle assembly checkpoint protein MAD2A
L: Mitotic spindle assembly checkpoint protein MAD2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8404
Polymers47,6482
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-35 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.829, 104.918, 157.746
Angle α, β, γ (deg.)90.00, 97.57, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
12
22
32
42
52
62
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 10:202)
211chain C and (resseq 10:44 or resseq 46:204)
311chain E and (resseq 10:204)
411chain G and (resseq 10:203)
511chain I and (resseq 10:32 or resseq 44:135 or resseq 143:203)
611chain K and (resseq 10:203)
112chain B
212chain D
312chain F and (resseq 10:46 or resseq 51:198)
412chain H and (resseq 10:157 or resseq 176:203)
512chain J and not (resseq 165 and (name CB or name CG or name CD or name OE*))
612chain L and (resseq 10:157 or resseq 176:198)
113chain H and (resseq 163:172)
213chain L and (resseq 163:172)

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Mitotic spindle assembly checkpoint protein MAD2A / MAD2-like 1 / HsMAD2


Mass: 23824.131 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAD2, MAD2A, MAD2L1 / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: Q13257
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jan 1, 2004
RadiationMonochromator: Custom / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 3.95→50 Å / Num. obs: 35718 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 116.12 Å2 / Rmerge(I) obs: 0.165 / Net I/σ(I): 11.6
Reflection shellResolution: 3.95→4.09 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V64

2v64


Resolution: 3.95→49.735 Å / SU ML: -0 / Isotropic thermal model: ISOTROPIC, WITH TLS / σ(F): 1.36 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 1771 4.97 %
Rwork0.2182 --
obs0.2199 35601 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 113.136 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 413.72 Å2 / Biso mean: 156.85 Å2 / Biso min: 65.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.799 Å20 Å219.572 Å2
2--33.17 Å20 Å2
3----34.969 Å2
Refinement stepCycle: LAST / Resolution: 3.95→49.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18241 0 60 0 18301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818620
X-RAY DIFFRACTIONf_angle_d1.02325239
X-RAY DIFFRACTIONf_dihedral_angle_d17.0966775
X-RAY DIFFRACTIONf_chiral_restr0.0683014
X-RAY DIFFRACTIONf_plane_restr0.0043118
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1550X-RAY DIFFRACTIONPOSITIONAL
12C1550X-RAY DIFFRACTIONPOSITIONAL0.028
13E1507X-RAY DIFFRACTIONPOSITIONAL0.039
14G1518X-RAY DIFFRACTIONPOSITIONAL0.033
15I1370X-RAY DIFFRACTIONPOSITIONAL0.04
16K1518X-RAY DIFFRACTIONPOSITIONAL0.036
21B1495X-RAY DIFFRACTIONPOSITIONAL
22D1495X-RAY DIFFRACTIONPOSITIONAL0.03
23F1414X-RAY DIFFRACTIONPOSITIONAL0.042
24H1342X-RAY DIFFRACTIONPOSITIONAL0.036
25J1490X-RAY DIFFRACTIONPOSITIONAL0.038
26L1299X-RAY DIFFRACTIONPOSITIONAL0.043
31H81X-RAY DIFFRACTIONPOSITIONAL
32L81X-RAY DIFFRACTIONPOSITIONAL0.017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.95-4.05680.32181170.27742474X-RAY DIFFRACTION95
4.0568-4.17610.25311190.24062613X-RAY DIFFRACTION100
4.1761-4.31080.25981340.22332587X-RAY DIFFRACTION100
4.3108-4.46480.2421230.20822602X-RAY DIFFRACTION100
4.4648-4.64340.2411390.19532606X-RAY DIFFRACTION100
4.6434-4.85460.21681250.19692594X-RAY DIFFRACTION100
4.8546-5.11030.21511400.18642613X-RAY DIFFRACTION100
5.1103-5.43010.2251510.19392604X-RAY DIFFRACTION100
5.4301-5.84870.23651370.2062596X-RAY DIFFRACTION100
5.8487-6.43620.2371510.21222590X-RAY DIFFRACTION100
6.4362-7.3650.23541450.2042630X-RAY DIFFRACTION100
7.365-9.26930.22171460.17952627X-RAY DIFFRACTION100
9.2693-49.73880.23821440.21432694X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined2.591.2705-0.69184.0035-1.20023.38470.12010.0356-0.4951-0.17380.0396-0.28350.358-0.2116-0.10790.84430.0678-0.39050.7762-0.24331.129693.9151-13.072755.3166
23.1794-0.4276-1.39261.9232-0.3241.72690.26190.29390.1982-0.2431-0.1746-0.3064-0.0898-0.3109-0.05120.88270.2556-0.07330.7151-0.07610.9398
33.38031.0492-0.26241.25981.84094.33890.29420.00890.7347-0.2274-0.03650.4096-0.7115-0.0686-0.33290.8794-0.08290.24650.57930.18151.354
42.1184-1.47671.89242.2504-0.28612.59250.36090.19330.0661-0.1128-0.20620.21790.01480.4245-0.05150.71910.05180.0140.7250.15190.9761
51.4272-1.3645-1.58973.5778-0.66345.14590.0755-1.33650.18750.69370.3676-0.52250.17441.9906-0.46411.0432-0.2287-0.11112.5192-0.47221.1351
63.5791-0.7555-1.99392.7617-1.03724.80.89790.53730.2903-0.57420.0894-0.22830.02590.3043-0.79031.2432-0.1290.23571.3634-0.18881.0854
72.6879-0.3220.0220.75370.30110.14790.25511.49940.0836-0.4608-0.042-0.1-0.16350.3515-0.11841.6820.1768-0.08582.12430.14261.0538
84.1350.20810.60870.09630.70634.36670.22810.11350.43540.348-0.3081-0.2379-0.5885-0.29940.08551.45510.1102-0.25060.81690.19421.1901
93.2219-1.5881-1.96352.80980.29053.7693-0.0132-0.05620.21630.29790.4828-0.0257-0.2282-0.7875-0.42031.5866-0.11190.19011.55650.21011.1546
101.7412-1.18651.69030.9917-0.52292.99950.43770.5871-0.0007-0.5833-0.07320.14440.72180.4149-0.18681.8921-0.2315-0.03111.50190.2090.9521
113.9267-0.24641.3314.27840.40250.8135-0.14592.02610.1538-0.5249-0.12960.1345-0.0051-0.00650.21831.106-0.15090.10442.2129-0.00191.0359
124.49531.0129-0.46880.13660.01085.7317-0.10610.0772-0.33390.2229-0.02730.53520.87680.66380.11931.20740.26730.2560.7679-0.08471.0947
Refinement TLS groupSelection details: chain L

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