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- PDB-6mf4: Crystal structure of the polo-box domain of Cdc5 from budding yeast. -

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Basic information

Entry
Database: PDB / ID: 6mf4
TitleCrystal structure of the polo-box domain of Cdc5 from budding yeast.
ComponentsCell cycle serine/threonine-protein kinase CDC5/MSD2
KeywordsCELL CYCLE / Transferase / Mitosis / Polo-like kinase / Cdc5 / Dbf4 / Spc72
Function / homology
Function and homology information


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 / Golgi Cisternae Pericentriolar Stack Reorganization / negative regulation of protein localization to nucleolus / Resolution of Sister Chromatid Cohesion ...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 / Golgi Cisternae Pericentriolar Stack Reorganization / negative regulation of protein localization to nucleolus / Resolution of Sister Chromatid Cohesion / meiotic spindle assembly / synaptonemal complex disassembly / centromeric DNA binding / polo kinase / resolution of meiotic recombination intermediates / cellular bud neck / exit from mitosis / spindle pole body / positive regulation of Rho protein signal transduction / mitotic spindle organization / phosphoprotein binding / kinetochore / spindle pole / protein kinase activity / cell division / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGuarne, A. / Almawi, A.W.
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 / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,5943
Polymers33,4631
Non-polymers1312
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.080, 65.950, 96.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33463.184 Da / Num. of mol.: 1
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 BL21 (bacteria) / References: UniProt: P32562, polo kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris pH 8.5, 20 % PEG3350, 200 mM sodium formate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.28341 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28341 Å / Relative weight: 1
ReflectionResolution: 1.8→48.1 Å / Num. obs: 30819 / % possible obs: 100 % / Redundancy: 4 % / CC1/2: 0.997 / Net I/σ(I): 12.58
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 2611 / CC1/2: 0.358

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q4O

1q4o


Resolution: 1.8→48.06 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.97
RfactorNum. reflection% reflection
Rfree0.197 1541 5 %
Rwork0.181 --
obs0.181 30819 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 2 234 2099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041959
X-RAY DIFFRACTIONf_angle_d0.8852658
X-RAY DIFFRACTIONf_dihedral_angle_d13.427697
X-RAY DIFFRACTIONf_chiral_restr0.034293
X-RAY DIFFRACTIONf_plane_restr0.004336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.85810.34291370.28512611X-RAY DIFFRACTION100
1.8581-1.92450.24431390.25592631X-RAY DIFFRACTION100
1.9245-2.00160.25541370.21512609X-RAY DIFFRACTION100
2.0016-2.09270.20951390.19162650X-RAY DIFFRACTION100
2.0927-2.2030.21311370.17992606X-RAY DIFFRACTION100
2.203-2.3410.18911400.17452649X-RAY DIFFRACTION100
2.341-2.52180.17981390.1772635X-RAY DIFFRACTION100
2.5218-2.77550.2051400.1792668X-RAY DIFFRACTION100
2.7755-3.17710.19831410.17662674X-RAY DIFFRACTION100
3.1771-4.00250.17061420.1692709X-RAY DIFFRACTION100
4.0025-48.07710.17991500.1622836X-RAY DIFFRACTION100

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