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- PDB-2qyf: Crystal structure of the Mad2/p31(comet)/Mad2-binding peptide ter... -

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Basic information

Entry
Database: PDB / ID: 2qyf
TitleCrystal structure of the Mad2/p31(comet)/Mad2-binding peptide ternary complex
Components
  • MAD2L1-binding protein
  • Mitotic spindle assembly checkpoint protein MAD2A
  • peptide
KeywordsCELL CYCLE / PROTEIN-PEPTIDE COMPLEX / MAD2 FAMILY / SPINDLE ASSEMBLY CHECKPOINT / Cell division / Mitosis / Nucleus / Phosphorylation
Function / homology
Function and homology information


deactivation of mitotic spindle assembly checkpoint / 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 / regulation of exit from mitosis / nuclear pore nuclear basket ...deactivation of mitotic spindle assembly checkpoint / 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 / regulation of exit from mitosis / nuclear pore nuclear basket / negative regulation of mitotic cell cycle / negative regulation of ubiquitin protein ligase activity / mitotic spindle assembly checkpoint signaling / 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 / spindle pole / mitotic spindle / Separation of Sister Chromatids / nuclear membrane / cell division / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A - #20 / Mad1/Cdc20-bound-Mad2 binding protein / : / Mad1 and Cdc20-bound-Mad2 binding / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. ...Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A - #20 / Mad1/Cdc20-bound-Mad2 binding protein / : / Mad1 and Cdc20-bound-Mad2 binding / 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 / MAD2L1-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsTomchick, D.R. / Luo, X.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2007
Title: p31comet blocks Mad2 activation through structural mimicry.
Authors: Yang, M. / Li, B. / Tomchick, D.R. / Machius, M. / Rizo, J. / Yu, H. / Luo, X.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: The Mad2 spindle checkpoint protein has two distinct natively folded states.
Authors: Luo, X. / Tang, Z. / Xia, G. / Wassmann, K. / Matsumoto, T. / Rizo, J. / Yu, H.
#2: Journal: Mol.Cell / Year: 2002
Title: The Mad2 Spindle Checkpoint Protein Undergoes Similar Major Conformational Changes Upon Binding to Either Mad1 or Cdc20
Authors: Luo, X. / Tang, Z. / Rizo, J. / Yu, H.
#3: Journal: Nat.Struct.Mol.Biol. / Year: 2000
Title: Structure of the Mad2 spindle assembly checkpoint protein and its interaction with Cdc20.
Authors: Luo, X. / Fang, G. / Coldiron, M. / Lin, Y. / Yu, H. / Kirschner, M.W. / Wagner, G.
History
DepositionAug 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitotic spindle assembly checkpoint protein MAD2A
B: MAD2L1-binding protein
C: Mitotic spindle assembly checkpoint protein MAD2A
D: MAD2L1-binding protein
E: peptide
F: peptide


Theoretical massNumber of molelcules
Total (without water)105,4716
Polymers105,4716
Non-polymers00
Water11,854658
1
A: Mitotic spindle assembly checkpoint protein MAD2A
B: MAD2L1-binding protein
E: peptide


Theoretical massNumber of molelcules
Total (without water)52,7353
Polymers52,7353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
2
C: Mitotic spindle assembly checkpoint protein MAD2A
D: MAD2L1-binding protein
F: peptide


Theoretical massNumber of molelcules
Total (without water)52,7353
Polymers52,7353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
Unit cell
Length a, b, c (Å)68.667, 104.519, 138.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 23595.750 Da / Num. of mol.: 2 / Mutation: L13A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAD2L1, MAD2 / Plasmid: pETDuet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13257
#2: Protein MAD2L1-binding protein / Caught by MAD2 protein


Mass: 27687.914 Da / Num. of mol.: 2 / Fragment: UNP residues 36-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAD2L1BP, CMT2, KIAA0110 / Plasmid: pETDuet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15013
#3: Protein/peptide peptide


Mass: 1451.604 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic 12-mer
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.3→44.23 Å / Num. all: 44434 / Num. obs: 44434 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 24.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 4 / Num. unique all: 2216 / Rsym value: 0.621 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.432 / SU ML: 0.16 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.306 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25673 1771 4 %RANDOM
Rwork0.18705 ---
all0.18985 43964 --
obs0.18985 42193 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.962 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2--0.37 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6286 0 0 658 6944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226433
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9678728
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7825768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99323.608291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1791545
X-RAY DIFFRACTIONr_chiral_restr0.1030.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024823
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.23100
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24422
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2559
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.09824037
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.10636357
X-RAY DIFFRACTIONr_scbond_it2.13622765
X-RAY DIFFRACTIONr_scangle_it3.0232371
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 129 -
Rwork0.199 3156 -
obs-3285 99.94 %

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