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- PDB-4yur: Crystal Structure of Plk4 Kinase Domain Bound to Centrinone -

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Basic information

Entry
Database: PDB / ID: 4yur
TitleCrystal Structure of Plk4 Kinase Domain Bound to Centrinone
ComponentsSerine/threonine-protein kinase PLK4
KeywordsTransferase/Transferase Inhibitor / Transferase / Protein Kinase / Inhibitor / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / procentriole replication complex / positive regulation of centriole replication / trophoblast giant cell differentiation / polo kinase / XY body / centriole replication / cleavage furrow ...de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / procentriole replication complex / positive regulation of centriole replication / trophoblast giant cell differentiation / polo kinase / XY body / centriole replication / cleavage furrow / cilium assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / mitotic spindle organization / kinetochore / spindle pole / Regulation of PLK1 Activity at G2/M Transition / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / ATP binding / identical protein binding / cytosol
Similarity search - Function
Serine/threonine-protein kinase, first cryptic polo-box domain superfamily / : / Cryptic Polo-Box 1 (CPB1) domain profile. / Cryptic Polo-Box 2 (CPB2) domain profile. / Plk4, C-terminal polo-box domain / Plk4, second cryptic polo-box domain / Plk4, first cryptic polo-box domain / Polo-like Kinase 4 Polo Box 1 / Polo-like Kinase 4 Polo Box 2 / POLO box domain ...Serine/threonine-protein kinase, first cryptic polo-box domain superfamily / : / Cryptic Polo-Box 1 (CPB1) domain profile. / Cryptic Polo-Box 2 (CPB2) domain profile. / Plk4, C-terminal polo-box domain / Plk4, second cryptic polo-box domain / Plk4, first cryptic polo-box domain / Polo-like Kinase 4 Polo Box 1 / Polo-like Kinase 4 Polo Box 2 / POLO box domain / POLO box domain profile. / Tyrosine-protein kinase, active site / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4J7 / Serine/threonine-protein kinase PLK4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsShiau, A.K. / Motamedi, A.
CitationJournal: Science / Year: 2015
Title: Cell biology. Reversible centriole depletion with an inhibitor of Polo-like kinase 4.
Authors: Wong, Y.L. / Anzola, J.V. / Davis, R.L. / Yoon, M. / Motamedi, A. / Kroll, A. / Seo, C.P. / Hsia, J.E. / Kim, S.K. / Mitchell, J.W. / Mitchell, B.J. / Desai, A. / Gahman, T.C. / Shiau, A.K. / Oegema, K.
History
DepositionMar 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2692
Polymers31,6361
Non-polymers6341
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.805, 125.805, 125.805
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Serine/threonine-protein kinase PLK4 / Polo-like kinase 4 / PLK-4 / Serine/threonine-protein kinase 18 / Serine/threonine-protein kinase Sak


Mass: 31635.566 Da / Num. of mol.: 1 / Fragment: UNP residues 2-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK4, SAK, STK18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2 (DE3) / References: UniProt: O00444, polo kinase
#2: Chemical ChemComp-4J7 / 2-({2-fluoro-4-[(2-fluoro-3-nitrobenzyl)sulfonyl]phenyl}sulfanyl)-5-methoxy-N-(3-methyl-1H-pyrazol-5-yl)-6-(morpholin-4-yl)pyrimidin-4-amine


Mass: 633.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25F2N7O6S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 0.2 M MgCl2, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.65→62.9 Å / Num. obs: 9793 / % possible obs: 100 % / Redundancy: 22.2 % / Biso Wilson estimate: 73.96 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 30.4
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 22.5 % / Rmerge(I) obs: 2.374 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3COK

3cok


Resolution: 2.65→62.9 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2695 469 4.79 %Random
Rwork0.1992 ---
obs0.2024 9782 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.07 Å2
Refinement stepCycle: LAST / Resolution: 2.65→62.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 43 12 1805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081833
X-RAY DIFFRACTIONf_angle_d1.3892481
X-RAY DIFFRACTIONf_dihedral_angle_d12.206659
X-RAY DIFFRACTIONf_chiral_restr0.071273
X-RAY DIFFRACTIONf_plane_restr0.004312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-3.0360.36541670.25263063X-RAY DIFFRACTION100
3.036-3.82490.27751460.22263080X-RAY DIFFRACTION100
3.8249-62.92020.24681560.18093170X-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)
11.946-0.938-1.88893.31571.37071.88490.20410.40110.453-0.5997-0.1227-0.0151-0.4678-0.24510.00350.5139-0.0112-0.06410.34930.0020.3438-19.368839.66648.0084
21.7717-1.9226-1.16183.8141.21221.47160.15610.08010.0789-0.3239-0.33160.1061-0.20770.2279-0.19490.2878-0.1384-0.04640.3736-0.05560.2194-8.462513.858244.6632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 265 )

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