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- PDB-6mf5: Crystal structure of budding yeast Cdc5 polo-box domain in comple... -

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Basic information

Entry
Database: PDB / ID: 6mf5
TitleCrystal structure of budding yeast Cdc5 polo-box domain in complex with Spc72 phosphopeptide.
Components
  • Cell cycle serine/threonine-protein kinase CDC5/MSD2
  • Spc72
KeywordsCELL CYCLE / Transferase / Mitosis / Dbf4 / Polo-like kinases
Function / homology
Function and homology information


gamma-tubulin complex localization to cytoplasmic side of mitotic spindle pole body / astral microtubule anchoring at mitotic spindle pole body / outer plaque of mitotic spindle pole body / positive regulation of mitotic spindle pole body separation / positive regulation of protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / regulation of protein localization to mitotic spindle pole body / Polo-like kinase mediated events / Regulation of PLK1 Activity at G2/M Transition / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / regulation of nucleus organization ...gamma-tubulin complex localization to cytoplasmic side of mitotic spindle pole body / astral microtubule anchoring at mitotic spindle pole body / outer plaque of mitotic spindle pole body / positive regulation of mitotic spindle pole body separation / positive regulation of protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / regulation of protein localization to mitotic spindle pole body / Polo-like kinase mediated events / Regulation of PLK1 Activity at G2/M Transition / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / regulation of nucleus organization / mitotic spindle orientation checkpoint signaling / Golgi Cisternae Pericentriolar Stack Reorganization / outer plaque of spindle pole body / negative regulation of protein localization to nucleolus / Resolution of Sister Chromatid Cohesion / meiotic spindle assembly / mitotic spindle astral microtubule end / karyogamy / synaptonemal complex disassembly / astral microtubule organization / centromeric DNA binding / polo kinase / resolution of meiotic recombination intermediates / microtubule nucleation / cellular bud neck / microtubule plus-end binding / spindle pole body / exit from mitosis / microtubule lateral binding / positive regulation of Rho protein signal transduction / cytoplasmic microtubule organization / mitotic spindle organization / phosphoprotein binding / spindle microtubule / kinetochore / spindle pole / protein kinase activity / phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Mto2p-binding domain / Micro-tubular organiser Mto1 C-term Mto2-binding region / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Mto2p-binding domain / Micro-tubular organiser Mto1 C-term Mto2-binding region / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / 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
Cell cycle serine/threonine-protein kinase CDC5/MSD2 / Spindle pole component SPC72
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGuarne, A. / Almawi, A.W.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Sci Rep / Year: 2020
Title: Distinct surfaces on Cdc5/PLK Polo-box domain orchestrate combinatorial substrate recognition during cell division.
Authors: Almawi, A.W. / Langlois-Lemay, L. / Boulton, S. / Rodriguez Gonzalez, J. / Melacini, G. / D'Amours, D. / Guarne, A.
History
DepositionSep 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell cycle serine/threonine-protein kinase CDC5/MSD2
B: Cell cycle serine/threonine-protein kinase CDC5/MSD2
C: Spc72
D: Spc72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2216
Polymers69,1504
Non-polymers712
Water19811
1
A: Cell cycle serine/threonine-protein kinase CDC5/MSD2
C: Spc72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6113
Polymers34,5752
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-16 kcal/mol
Surface area12910 Å2
MethodPISA
2
B: Cell cycle serine/threonine-protein kinase CDC5/MSD2
D: Spc72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6113
Polymers34,5752
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-14 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.470, 68.190, 86.230
Angle α, β, γ (deg.)90.00, 102.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell cycle serine/threonine-protein kinase CDC5/MSD2


Mass: 33463.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CDC5, MSD2, PKX2, YMR001C, YM8270.03C / Production host: Escherichia coli (E. coli) / References: UniProt: P32562, polo kinase
#2: Protein/peptide Spc72


Mass: 1112.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: synthetic construct (others) / References: UniProt: P39723*PLUS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris pH 6.50, 200 mM magnesium chloride, 100 mM cesium chloride, 25 % PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→42.1 Å / Num. obs: 16158 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.99 / Net I/σ(I): 9.1
Reflection shellResolution: 2.7→2.78 Å / Num. unique obs: 1184 / CC1/2: 0.317

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q4O

1q4o


Resolution: 2.7→42.08 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.73
RfactorNum. reflection% reflection
Rfree0.261 1622 10.05 %
Rwork0.231 --
obs0.234 16142 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 0 2 11 3815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033930
X-RAY DIFFRACTIONf_angle_d0.85365
X-RAY DIFFRACTIONf_dihedral_angle_d13.7571283
X-RAY DIFFRACTIONf_chiral_restr0.029642
X-RAY DIFFRACTIONf_plane_restr0.004676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.77950.33861300.30071184X-RAY DIFFRACTION99
2.7795-2.86920.35811310.28811227X-RAY DIFFRACTION99
2.8692-2.97180.33411360.28031196X-RAY DIFFRACTION100
2.9718-3.09070.35751390.27971182X-RAY DIFFRACTION100
3.0907-3.23130.30381340.27531230X-RAY DIFFRACTION100
3.2313-3.40160.29641370.25591189X-RAY DIFFRACTION100
3.4016-3.61460.27241190.23241214X-RAY DIFFRACTION100
3.6146-3.89350.2511380.22441201X-RAY DIFFRACTION100
3.8935-4.2850.23851440.19531221X-RAY DIFFRACTION100
4.285-4.90420.19721360.17951194X-RAY DIFFRACTION100
4.9042-6.17570.23021360.22791239X-RAY DIFFRACTION100
6.1757-42.08340.24591420.22661243X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3587-0.1945-0.31040.60130.2118-0.19310.21250.1994-0.4091-0.3381-0.18780.3708-0.0691-0.17780.00470.27160.0252-0.02440.3958-0.04850.3251-37.472110.0543-24.4672
21.72350.3413-0.41354.35360.40712.5670.0408-0.14490.0520.3157-0.0533-0.103-0.0403-0.1908-0.00910.1996-0.0104-0.0210.2572-0.01220.1771-15.9463.7863-17.9049
32.46830.6751.1690.21180.33460.331-0.49510.38551.51650.3153-0.18790.12420.44530.1634-0.40430.4795-0.1065-0.10.32310.07250.5432-63.115547.506-32.7939
42.06170.6267-0.42342.89360.1592.0496-0.0268-0.09510.1433-0.173-0.0353-0.4268-0.30260.1763-0.00350.41480.0096-0.02490.30530.00470.3865-40.356835.1898-21.7661
50.0816-0.0983-0.03630.0680.04420.05050.1659-0.38140.5034-0.26620.6853-0.71080.0738-0.74410.00380.44540.00790.05420.5107-0.00440.6643-12.691717.5508-15.4297
60.31170.2132-0.00710.22920.13650.2193-0.3271-0.00090.22990.06610.0748-0.2664-0.0770.0409-0.04540.7912-0.04110.18110.45460.05791.3544-30.709248.0006-24.0516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 435 THROUGH 492 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 493 THROUGH 704 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 434 THROUGH 470 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 471 THROUGH 704 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 228 THROUGH 234 )
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID 228 THROUGH 234 )

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