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- PDB-7b1f: Orthorhombic P212121 Structure of Human Mad1 C-terminal Domain in... -

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Basic information

Entry
Database: PDB / ID: 7b1f
TitleOrthorhombic P212121 Structure of Human Mad1 C-terminal Domain in Complex with Phosphorylated Bub1 CD1 Domain
Components
  • Mitotic checkpoint serine/threonine-protein kinase BUB1
  • Mitotic spindle assembly checkpoint protein MAD1
KeywordsCELL CYCLE / mad1 / bub1 / mitotic checkpoint complex / spindle assembly checkpoint
Function / homology
Function and homology information


MAD1 complex / positive regulation of maintenance of mitotic sister chromatid cohesion, centromeric / histone H2A kinase activity / deactivation of mitotic spindle assembly checkpoint / mitotic spindle assembly checkpoint MAD1-MAD2 complex / regulation of sister chromatid cohesion / regulation of chromosome segregation / positive regulation of mitotic cell cycle spindle assembly checkpoint / meiotic sister chromatid cohesion, centromeric / kinetochore binding ...MAD1 complex / positive regulation of maintenance of mitotic sister chromatid cohesion, centromeric / histone H2A kinase activity / deactivation of mitotic spindle assembly checkpoint / mitotic spindle assembly checkpoint MAD1-MAD2 complex / regulation of sister chromatid cohesion / regulation of chromosome segregation / positive regulation of mitotic cell cycle spindle assembly checkpoint / meiotic sister chromatid cohesion, centromeric / kinetochore binding / nuclear pore nuclear basket / outer kinetochore / regulation of metaphase plate congression / attachment of mitotic spindle microtubules to kinetochore / mitotic spindle assembly checkpoint signaling / negative regulation of T cell proliferation / 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 / thymus development / chromosome segregation / RHO GTPases Activate Formins / kinetochore / spindle / spindle pole / mitotic spindle / Separation of Sister Chromatids / nuclear envelope / non-specific serine/threonine protein kinase / protein kinase activity / cell division / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / apoptotic process / centrosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Spindle assembly checkpoint component Mad1 / Mitotic checkpoint protein / Mad3/Bub1 homology region 1 / Mitotic spindle checkpoint protein Bub1/Mad3 / Mad3/BUB1 homology region 1 / BUB1 N-terminal domain profile. / Mad3/BUB1 hoMad3/BUB1 homology region 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Spindle assembly checkpoint component Mad1 / Mitotic checkpoint protein / Mad3/Bub1 homology region 1 / Mitotic spindle checkpoint protein Bub1/Mad3 / Mad3/BUB1 homology region 1 / BUB1 N-terminal domain profile. / Mad3/BUB1 hoMad3/BUB1 homology region 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Mitotic checkpoint serine/threonine-protein kinase BUB1 / Mitotic spindle assembly checkpoint protein MAD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFischer, E. / Bellini, D. / Barford, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: Embo Rep. / Year: 2021
Title: Molecular mechanism of Mad1 kinetochore targeting by phosphorylated Bub1.
Authors: Fischer, E.S. / Yu, C.W.H. / Bellini, D. / McLaughlin, S.H. / Orr, C.M. / Wagner, A. / Freund, S.M.V. / Barford, D.
History
DepositionNov 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: 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
Revision 1.4Nov 20, 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

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Assembly

Deposited unit
B: Mitotic spindle assembly checkpoint protein MAD1
A: Mitotic spindle assembly checkpoint protein MAD1
C: Mitotic checkpoint serine/threonine-protein kinase BUB1
D: Mitotic checkpoint serine/threonine-protein kinase BUB1


Theoretical massNumber of molelcules
Total (without water)33,9704
Polymers33,9704
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-70 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.219, 80.492, 133.998
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: 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: 13961.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAD1L1, MAD1, TXBP181 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y6D9
#2: Protein/peptide Mitotic checkpoint serine/threonine-protein kinase BUB1 / hBUB1 / BUB1A


Mass: 3023.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: O43683, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000, 0.1 M Hepes pH 7.5, 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→40.25 Å / Num. obs: 33937 / % possible obs: 89 % / Redundancy: 5.6 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Rrim(I) all: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 1.75→1.813 Å / Rmerge(I) obs: 1.97 / Num. unique obs: 1863 / CC1/2: 0.3 / Rpim(I) all: 1.2 / Rrim(I) all: 2.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DZO

4dzo


Resolution: 1.75→40.25 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2873 1569 4.77 %
Rwork0.2558 31318 -
obs0.2573 32887 85.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.96 Å2 / Biso mean: 56.9543 Å2 / Biso min: 23.75 Å2
Refinement stepCycle: final / Resolution: 1.75→40.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2269 0 0 139 2408
Biso mean---50.16 -
Num. residues----282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.810.3948620.44471080114233
1.81-1.870.4401850.38811775186055
1.87-1.950.4428900.46532129221965
1.95-2.030.35511390.31482952309189
2.03-2.140.30841750.27532553430100
2.14-2.280.31921650.303932643429100
2.28-2.450.26441650.265932973462100
2.45-2.70.30811830.270832883471100
2.7-3.090.28681490.269733613510100
3.09-3.890.28371660.24633733539100
3.89-40.250.26541900.221835443734100

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