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- PDB-2v64: Crystallographic structure of the conformational dimer of the Spi... -

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Basic information

Entry
Database: PDB / ID: 2v64
TitleCrystallographic structure of the conformational dimer of the Spindle Assembly Checkpoint protein Mad2.
Components
  • (MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A) x 2
  • MBP1
KeywordsCELL CYCLE / SPINDLE ASSEMBLY CHECKPOINT / MAD2 / NUCLEUS / MITOSIS / APOPTOSIS / CELL DIVISION / PHOSPHORYLATION / CONFORMATIONAL DIMER
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 mitotic cell cycle / 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 mitotic cell cycle / mitotic spindle assembly checkpoint signaling / negative regulation of ubiquitin protein ligase activity / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / APC-Cdc20 mediated degradation of Nek2A / Resolution of Sister Chromatid Cohesion / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / RHO GTPases Activate Formins / negative regulation of protein catabolic process / kinetochore / spindle pole / mitotic spindle / Separation of Sister Chromatids / cell division / 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)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMapelli, M. / Massimiliano, L. / Santaguida, S. / Musacchio, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: The MAD2 Conformational Dimer: Structure and Implications for the Spindle Assembly Checkpoint
Authors: Mapelli, M. / Massimiliano, L. / Santaguida, S. / Musacchio, A.
History
DepositionJul 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: MBP1
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: MBP1
H: MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A
I: MBP1


Theoretical massNumber of molelcules
Total (without water)149,1689
Polymers149,1689
Non-polymers00
Water1086
1
A: MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A
B: MBP1
E: MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A


Theoretical massNumber of molelcules
Total (without water)49,7233
Polymers49,7233
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-17.2 kcal/mol
Surface area19150 Å2
MethodPISA
2
C: MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A
D: MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A
I: MBP1


Theoretical massNumber of molelcules
Total (without water)49,7233
Polymers49,7233
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-18.81 kcal/mol
Surface area19290 Å2
MethodPISA
3
F: MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A
G: MBP1
H: MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A


Theoretical massNumber of molelcules
Total (without water)49,7233
Polymers49,7233
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-18.15 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.580, 111.880, 131.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.33906, -0.24022, 0.90958), (0.90672, 0.17431, 0.38403), (-0.2508, 0.95494, 0.15871)-7.2454, 2.385, 0.4897
2given(-0.34287, 0.9062, -0.24749), (-0.25919, 0.16198, 0.95215), (0.90292, 0.39061, 0.17934)-2.9211, 5.3961, -4.085

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Components

#1: Protein MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A / MAD2-LIKE 1 / HSMAD2 / MAD2


Mass: 24506.896 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q13257
#2: Protein/peptide MBP1


Mass: 1451.604 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: SEQUENCE SWYSYPPPQRAV / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Protein MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A / MAD2-LIKE 1 / HSMAD2 / MAD2


Mass: 23764.076 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-108,118-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q13257
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINAL HISTIDINE TAG IN CHAINS A, C, F. N-TERMINAL HISTIDINE TAG AND SUBSTITUTION OF RESIDUES ...N-TERMINAL HISTIDINE TAG IN CHAINS A, C, F. N-TERMINAL HISTIDINE TAG AND SUBSTITUTION OF RESIDUES 109- 117 WITH GSG IN CHAINS D, E, H.

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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: 2.8 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 4.6 / Details: 0.1M NAACETATE PH 4.6, 3.5M NAFORMATE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9333
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9333 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 37591 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 6.9 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 16.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GO4

1go4


Resolution: 2.9→29.44 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2539666.54 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1766 5 %RANDOM
Rwork0.233 ---
obs0.233 35593 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.5759 Å2 / ksol: 0.385076 e/Å3
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.19 Å20 Å20 Å2
2--0.21 Å20 Å2
3---3.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9642 0 0 6 9648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 303 5.2 %
Rwork0.308 5527 -
obs--94.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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