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- PDB-4yyp: Crystal structure of human PLK4-PB3 in complex with STIL-CC -

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Basic information

Entry
Database: PDB / ID: 4yyp
TitleCrystal structure of human PLK4-PB3 in complex with STIL-CC
Components
  • SCL-interrupting locus protein
  • Serine/threonine-protein kinase PLK4
KeywordsTRANSFERASE / Polo-box / Complex
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: 2.6 Å
AuthorsImseng, S. / Arquint, C. / Gabryjonczyk, A. / Boehm, R. / Sauer, E. / Hiller, S. / Nigg, E.A. / Maier, T.
CitationJournal: Elife / Year: 2015
Title: STIL binding to Polo-box 3 of PLK4 regulates centriole duplication.
Authors: Arquint, C. / Gabryjonczyk, A.M. / Imseng, S. / Bohm, R. / Sauer, E. / Hiller, S. / Nigg, E.A. / Maier, T.
History
DepositionMar 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK4
B: SCL-interrupting locus protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4553
Polymers13,4192
Non-polymers351
Water27015
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-22 kcal/mol
Surface area7580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.570, 136.330, 33.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 9572.777 Da / Num. of mol.: 1 / Fragment: residues 884-970
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK4, SAK, STK18 / Plasmid: pETG-30A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00444, polo kinase
#2: Protein/peptide SCL-interrupting locus protein / TAL-1-interrupting locus protein


Mass: 3846.417 Da / Num. of mol.: 1 / Fragment: residues 720-751 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15468
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.68 Å3/Da / Density % sol: 66.64 % / Description: Thin, plate-like crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Thin needles grew in precipitant solution containing 100 mM Hepes, pH 7.0, 20 mM MgCl2 and 22% Poly(acrylic acid sodium salt) 5100. After extensive optimization and seeding plate-like ...Details: Thin needles grew in precipitant solution containing 100 mM Hepes, pH 7.0, 20 mM MgCl2 and 22% Poly(acrylic acid sodium salt) 5100. After extensive optimization and seeding plate-like crystals were grown in a drop consisting of 50% PLK4-PB3/STIL-CC complex solution, 33.3% precipitant solution (100 mM phosphate/citrate pH 4.2, 40% (v/v) Ethanol, 5% (w/v) PEG 1000) and 16.7% of seed stock solution.
PH range: 4.2 - 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→68.1 Å / Num. obs: 6428 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 89.04 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.3
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 6.6 % / Rmerge(I) obs: 2.37 / Mean I/σ(I) obs: 0.9 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
PHASERphasing
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P34

3p34


Resolution: 2.6→20.8 Å / Cor.coef. Fo:Fc: 0.8892 / Cor.coef. Fo:Fc free: 0.8788 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.354 / SU Rfree Blow DPI: 0.255
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 631 9.85 %RANDOM
Rwork0.2174 ---
obs0.2208 6409 99.72 %-
Displacement parametersBiso mean: 89.61 Å2
Baniso -1Baniso -2Baniso -3
1-27.6337 Å20 Å20 Å2
2---56.763 Å20 Å2
3---29.1294 Å2
Refine analyzeLuzzati coordinate error obs: 0.504 Å
Refinement stepCycle: 1 / Resolution: 2.6→20.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 1 15 1845
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011848HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.153304HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d413SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes29HARMONIC2
X-RAY DIFFRACTIONt_gen_planes265HARMONIC5
X-RAY DIFFRACTIONt_it1848HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion18.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion125SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2037SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.91 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.379 190 10.71 %
Rwork0.2969 1584 -
all0.3055 1774 -
obs--99.72 %

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