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- PDB-5lhz: PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL -

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Basic information

Entry
Database: PDB / ID: 5lhz
TitlePB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL
Components
  • SCL-interrupting locus protein
  • Serine/threonine-protein kinase PLK4
KeywordsSTRUCTURAL PROTEIN / Polo box domain / Centriole / Complex / transferase
Function / homology
Function and homology information


floor plate development / de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / trophoblast giant cell differentiation / embryonic axis specification / positive regulation of spindle assembly ...floor plate development / de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / trophoblast giant cell differentiation / embryonic axis specification / positive regulation of spindle assembly / notochord development / polo kinase / XY body / determination of left/right symmetry / protein localization to centrosome / neural tube development / smoothened signaling pathway / heart looping / centriole replication / cleavage furrow / centrosome duplication / cilium assembly / positive regulation of G1/S transition of mitotic cell cycle / regulation of mitotic spindle organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / forebrain development / 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 / neural tube closure / multicellular organism growth / kinetochore / spindle pole / Regulation of PLK1 Activity at G2/M Transition / cell cortex / in utero embryonic development / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / negative regulation of apoptotic process / nucleoplasm / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
SCL-interrupting locus protein / SCL-interrupting locus protein N-terminus / 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 ...SCL-interrupting locus protein / SCL-interrupting locus protein N-terminus / 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 / POLO box domain profile. / Arylsulfatase, C-terminal domain / Tyrosine-protein kinase, active site / 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 / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PLK4 / SCL-interrupting locus protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsCottee, M.A. / Lea, S.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust100298 United Kingdom
Wellcome Trust104575 United Kingdom
CitationJournal: Biol Open / Year: 2017
Title: A key centriole assembly interaction interface between human PLK4 and STIL appears to not be conserved in flies.
Authors: Cottee, M.A. / Johnson, S. / Raff, J.W. / Lea, S.M.
History
DepositionJul 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3May 10, 2017Group: Database references
Revision 1.4Jan 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK4
B: Serine/threonine-protein kinase PLK4
C: Serine/threonine-protein kinase PLK4
D: SCL-interrupting locus protein
E: SCL-interrupting locus protein
F: SCL-interrupting locus protein


Theoretical massNumber of molelcules
Total (without water)39,3456
Polymers39,3456
Non-polymers00
Water905
1
A: Serine/threonine-protein kinase PLK4
D: SCL-interrupting locus protein


Theoretical massNumber of molelcules
Total (without water)13,1152
Polymers13,1152
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-10 kcal/mol
Surface area6250 Å2
MethodPISA
2
B: Serine/threonine-protein kinase PLK4
E: SCL-interrupting locus protein


Theoretical massNumber of molelcules
Total (without water)13,1152
Polymers13,1152
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-12 kcal/mol
Surface area6160 Å2
MethodPISA
3
C: Serine/threonine-protein kinase PLK4
F: SCL-interrupting locus protein


Theoretical massNumber of molelcules
Total (without water)13,1152
Polymers13,1152
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-10 kcal/mol
Surface area6020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.360, 68.360, 137.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: 9915.191 Da / Num. of mol.: 3 / Fragment: UNP residues 884-970
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK4, SAK, STK18 / Production host: Escherichia coli B (bacteria) / Strain (production host): B834 / References: UniProt: O00444, polo kinase
#2: Protein/peptide SCL-interrupting locus protein / TAL-1-interrupting locus protein


Mass: 3199.662 Da / Num. of mol.: 3 / Fragment: UNP residues 726-750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STIL, SIL / Production host: Escherichia coli B (bacteria) / Strain (production host): C41 / References: UniProt: Q15468
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.36 Å3/Da / Density % sol: 47.78 % / Description: Hexagonal rod
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.51→36.223 Å / Num. obs: 13265 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.995 / Net I/σ(I): 12.1
Reflection shellHighest resolution: 2.51 Å / Rmerge(I) obs: 1.312

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model based on 4YYP

4yyp


Resolution: 2.51→36.223 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.21
RfactorNum. reflection% reflection
Rfree0.2821 669 5.06 %
Rwork0.2496 --
obs0.2513 13232 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.51→36.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 0 5 2342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022367
X-RAY DIFFRACTIONf_angle_d0.4323196
X-RAY DIFFRACTIONf_dihedral_angle_d11.5951436
X-RAY DIFFRACTIONf_chiral_restr0.039374
X-RAY DIFFRACTIONf_plane_restr0.002404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5103-2.70410.38411220.35432480X-RAY DIFFRACTION100
2.7041-2.97610.37571300.29612472X-RAY DIFFRACTION100
2.9761-3.40650.32481570.26362447X-RAY DIFFRACTION100
3.4065-4.29070.24951370.22632514X-RAY DIFFRACTION100
4.2907-36.22710.25761230.2382650X-RAY DIFFRACTION100

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