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- PDB-7b1h: Monoclinic P21 Structure of Human Mad1 C-terminal Domain in Compl... -

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Basic information

Entry
Database: PDB / ID: 7b1h
TitleMonoclinic P21 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 / spindle assembly checkpoint / mitotic checkpoint complex
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: 2.4 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 13, 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
E: Mitotic spindle assembly checkpoint protein MAD1
F: Mitotic spindle assembly checkpoint protein MAD1
G: Mitotic checkpoint serine/threonine-protein kinase BUB1
H: Mitotic checkpoint serine/threonine-protein kinase BUB1


Theoretical massNumber of molelcules
Total (without water)67,9408
Polymers67,9408
Non-polymers00
Water21612
1
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-78 kcal/mol
Surface area15290 Å2
MethodPISA
2
E: Mitotic spindle assembly checkpoint protein MAD1
F: Mitotic spindle assembly checkpoint protein MAD1
G: Mitotic checkpoint serine/threonine-protein kinase BUB1
H: Mitotic checkpoint serine/threonine-protein kinase BUB1


Theoretical massNumber of molelcules
Total (without water)33,9704
Polymers33,9704
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-73 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.630, 132.340, 82.750
Angle α, β, γ (deg.)90.00, 93.34, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAD1L1, MAD1, TXBP181 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6D9
#2: Protein/peptide
Mitotic checkpoint serine/threonine-protein kinase BUB1 / hBUB1 / BUB1A


Mass: 3023.290 Da / Num. of mol.: 4 / 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.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8% Isopropanol, 20% PEG 4000, 0.1 M Na HEPES, pH 7.5

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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: 2.4→39.43 Å / Num. obs: 100346 / % possible obs: 99.56 % / Redundancy: 3.5 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.04 / Rrim(I) all: 0.07 / Net I/σ(I): 14.5
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4893 / CC1/2: 0.68 / Rpim(I) all: 0.04 / Rrim(I) all: 0.07 / % possible all: 99.04

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
xia2data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DZO

4dzo


Resolution: 2.4→39.43 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2806 1376 4.75 %
Rwork0.2314 --
obs0.2337 28946 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 0 12 4542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144604
X-RAY DIFFRACTIONf_angle_d1.9056202
X-RAY DIFFRACTIONf_dihedral_angle_d26.2611736
X-RAY DIFFRACTIONf_chiral_restr0.089717
X-RAY DIFFRACTIONf_plane_restr0.005779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.490.36311100.32472788X-RAY DIFFRACTION99
2.49-2.590.39021210.29662745X-RAY DIFFRACTION100
2.59-2.70.35321360.28312749X-RAY DIFFRACTION100
2.7-2.850.36111590.27842744X-RAY DIFFRACTION100
2.85-3.020.33381320.26542733X-RAY DIFFRACTION100
3.02-3.260.28731390.24582775X-RAY DIFFRACTION100
3.26-3.580.33251500.24032743X-RAY DIFFRACTION100
3.58-4.10.24341400.21992743X-RAY DIFFRACTION99
4.1-5.170.24231200.19812797X-RAY DIFFRACTION100
5.17-39.430.23911690.20712753X-RAY DIFFRACTION99

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