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- PDB-7b1j: Orthorhombic P21212 Structure of Human Mad1 C-terminal Domain in ... -

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Basic information

Entry
Database: PDB / ID: 7b1j
TitleOrthorhombic P21212 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 / histone H2A kinase activity / positive regulation of maintenance of mitotic sister chromatid cohesion, centromeric / 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 / regulation of metaphase plate congression / meiotic sister chromatid cohesion, centromeric ...MAD1 complex / histone H2A kinase activity / positive regulation of maintenance of mitotic sister chromatid cohesion, centromeric / 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 / regulation of metaphase plate congression / meiotic sister chromatid cohesion, centromeric / cytoplasmic sequestering of protein / kinetochore binding / outer kinetochore / nuclear pore nuclear basket / attachment of mitotic spindle microtubules to kinetochore / mitotic spindle assembly checkpoint signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of T cell proliferation / Resolution of Sister Chromatid Cohesion / thymus development / chromosome segregation / RHO GTPases Activate Formins / kinetochore / spindle / mitotic spindle / spindle pole / Separation of Sister Chromatids / nuclear envelope / non-specific serine/threonine protein kinase / protein kinase activity / cell division / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / centrosome / apoptotic process / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
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: 2.9 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 25, 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)33,8104
Polymers33,8104
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-73 kcal/mol
Surface area15650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.680, 133.980, 34.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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 (E. coli) / References: UniProt: Q9Y6D9
#2: Protein/peptide Mitotic checkpoint serine/threonine-protein kinase BUB1 / hBUB1 / BUB1A


Mass: 2943.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BUB1, BUB1L / Production host: Escherichia coli (E. coli)
References: UniProt: O43683, non-specific serine/threonine protein kinase
Has ligand of interestN

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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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% Isopropanol, 0.1 M Na HEPES, pH 7.5, 20% PEG 4000

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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: 2.9→34.75 Å / Num. obs: 9638 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 89.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Net I/σ(I): 25.9
Reflection shellResolution: 2.9→3.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 454 / CC1/2: 0.977 / Rpim(I) all: 0.0196 / Rrim(I) all: 0.51 / % possible all: 99.6

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Processing

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

4dzo


Resolution: 2.9→34.75 Å / SU ML: 0.4758 / Cross valid method: FREE R-VALUE / Phase error: 41.0685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2961 480 5.03 %
Rwork0.261 9061 -
obs0.263 9541 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.52 Å2
Refinement stepCycle: LAST / Resolution: 2.9→34.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 0 0 2262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02452297
X-RAY DIFFRACTIONf_angle_d2.33033093
X-RAY DIFFRACTIONf_chiral_restr0.1572358
X-RAY DIFFRACTIONf_plane_restr0.0101389
X-RAY DIFFRACTIONf_dihedral_angle_d20.5326865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.320.40141500.36742906X-RAY DIFFRACTION98.71
3.32-4.180.36261570.30282993X-RAY DIFFRACTION99.18
4.18-34.750.2571730.23033162X-RAY DIFFRACTION99.7

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