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- PDB-1go4: Crystal structure of Mad1-Mad2 reveals a conserved Mad2 binding m... -

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Basic information

Entry
Database: PDB / ID: 1go4
TitleCrystal structure of Mad1-Mad2 reveals a conserved Mad2 binding motif in Mad1 and Cdc20.
Components
  • Mitotic spindle assembly checkpoint protein MAD1
  • Mitotic spindle assembly checkpoint protein MAD2A
KeywordsCELL CYCLE / MITOTIC SPINDLE CHECKPOINT / MITOSIS / NUCLEAR PRO
Function / homology
Function and homology information


MAD1 complex / 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 / regulation of metaphase plate congression / establishment of centrosome localization / cytoplasmic sequestering of protein / Inactivation of APC/C via direct inhibition of the APC/C complex ...MAD1 complex / 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 / regulation of metaphase plate congression / establishment of centrosome localization / cytoplasmic sequestering of protein / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / kinetochore binding / nuclear pore nuclear basket / attachment of mitotic spindle microtubules to kinetochore / negative regulation of ubiquitin protein ligase activity / mitotic spindle assembly checkpoint signaling / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / negative regulation of mitotic cell cycle / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / negative regulation of T cell proliferation / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / APC-Cdc20 mediated degradation of Nek2A / thymus development / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / negative regulation of protein catabolic process / mitotic spindle / kinetochore / spindle pole / spindle / Separation of Sister Chromatids / nuclear envelope / cell division / centrosome / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #90 / Spindle assembly checkpoint component Mad1 / Mitotic checkpoint protein / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #90 / Spindle assembly checkpoint component Mad1 / Mitotic checkpoint protein / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Mitotic spindle assembly checkpoint protein MAD2A / Mitotic spindle assembly checkpoint protein MAD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.05 Å
AuthorsSironi, L. / Mapelli, M. / Jeang, K.T. / Musacchio, A.
CitationJournal: EMBO J. / Year: 2002
Title: Crystal structure of the tetrameric Mad1-Mad2 core complex: implications of a 'safety belt' binding mechanism for the spindle checkpoint.
Authors: Sironi, L. / Mapelli, M. / Knapp, S. / De Antoni, A. / Jeang, K.T. / Musacchio, A.
History
DepositionOct 17, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jun 20, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.pdbx_mutation / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.6Oct 16, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.7Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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 MAD1
F: Mitotic spindle assembly checkpoint protein MAD1
G: Mitotic spindle assembly checkpoint protein MAD1
H: Mitotic spindle assembly checkpoint protein MAD1


Theoretical massNumber of molelcules
Total (without water)140,5638
Polymers140,5638
Non-polymers00
Water11,313628
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)111.037, 63.023, 139.511
Angle α, β, γ (deg.)90.00, 111.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Mitotic spindle assembly checkpoint protein MAD2A / HsMAD2 / Mitotic arrest deficient 2-like protein 1 / MAD2-like protein 1


Mass: 23447.768 Da / Num. of mol.: 4 / Mutation: R133A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: DICISTRONIC VECTOR / Gene: MAD2L1, MAD2 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1BLUE / References: UniProt: Q13257
#2: Protein
Mitotic spindle assembly checkpoint protein MAD1 / Mitotic arrest deficient 1-like protein 1 / MAD1-like protein 1 / Mitotic checkpoint MAD1 protein ...Mitotic arrest deficient 1-like protein 1 / MAD1-like protein 1 / Mitotic checkpoint MAD1 protein homolog / hMAD1 / Tax-binding protein 181


Mass: 11693.103 Da / Num. of mol.: 4 / Fragment: RESIDUES 485-584
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: DICISTRONIC VECTOR / Gene: MAD1L1, MAD1, TXBP181 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1BLUE / References: UniProt: Q9Y6D9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B, C, D ENGINEERED MUTATION ARG133ALA REQUIRED FOR THE EXECUTION OF THE MITOTIC CHECKPOINT

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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: 3.08 Å3/Da / Density % sol: 60 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.2
Details: PROTEIN CONCENTRATION 7.5 MG/ML HANGING DROP METHOD, WELL=100 MM AMMONIUM SULPHATE, 100 MM AMMONIUM CITRATE PH 5.2, 10 MM DTT
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17.5 mg/mlprotein1drop
2100 mMammonium sulfate1reservoir
3100 mMsodium citrate1reservoirpH5.2
410 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 113010 / % possible obs: 99.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 18.2
Reflection shellResolution: 2.05→2.18 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.96 / % possible all: 90
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 368557
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SIRAS
Starting model: 1DUJ

1duj


Resolution: 2.05→24.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2022904.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 5665 5 %RANDOM
Rwork0.24 ---
obs0.24 112652 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.0425 Å2 / ksol: 0.354336 e/Å3
Displacement parametersBiso mean: 63.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.63 Å20 Å20.2 Å2
2---0.43 Å20 Å2
3----2.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.05→24.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9300 0 0 628 9928
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.671.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it2.772
X-RAY DIFFRACTIONc_scangle_it3.822.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 946 5.1 %
Rwork0.278 17599 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAM
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.24 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.88
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.76
LS refinement shell
*PLUS
Rfactor obs: 0.278

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