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- PDB-6n45: Crystal structure of the cryptic polo box domain of human activat... -

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Basic information

Entry
Database: PDB / ID: 6n45
TitleCrystal structure of the cryptic polo box domain of human activated Plk4 variant 1
ComponentsChimera protein of Serine/threonine-protein kinase PLK4 and DDB1- and CUL4-associated factor 1
KeywordsCELL CYCLE / Polo-like kinase 4 / protein phosphorylation / centriole duplication / PCM organization / phase separation
Function / homology
Function and homology information


de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / trophoblast giant cell differentiation / procentriole replication complex / cell competition in a multicellular organism / positive regulation of centriole replication / polo kinase / V(D)J recombination / XY body ...de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / trophoblast giant cell differentiation / procentriole replication complex / cell competition in a multicellular organism / positive regulation of centriole replication / polo kinase / V(D)J recombination / XY body / Cul4-RING E3 ubiquitin ligase complex / centriole replication / cleavage furrow / cilium assembly / ubiquitin-like ligase-substrate adaptor activity / centriole / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / post-translational protein modification / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / B cell differentiation / AURKA Activation by TPX2 / nuclear estrogen receptor binding / fibrillar center / positive regulation of protein catabolic process / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein ubiquitination / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Arylsulfatase, C-terminal domain - #120 / Arylsulfatase, C-terminal domain - #130 / 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 / Cryptic Polo-Box 1 (CPB1) domain profile. / Cryptic Polo-Box 2 (CPB2) domain profile. / Serine/threonine-protein kinase, first cryptic polo-box domain superfamily ...Arylsulfatase, C-terminal domain - #120 / Arylsulfatase, C-terminal domain - #130 / 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 / Cryptic Polo-Box 1 (CPB1) domain profile. / Cryptic Polo-Box 2 (CPB2) domain profile. / Serine/threonine-protein kinase, first cryptic polo-box domain superfamily / : / VPRBP/DCAF1 family / POLO box domain / POLO box domain profile. / Arylsulfatase, C-terminal domain / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Armadillo-like helical / Tyrosine-protein kinase, active site / Armadillo-type fold / WD40-repeat-containing domain superfamily / Protein kinase domain / WD40/YVTN repeat-like-containing domain superfamily / 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 / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsZhang, L. / Park, J.-E. / Meng, L. / Lee, K.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural grant United States
CitationJournal: Nat Commun / Year: 2019
Title: Phase separation of Polo-like kinase 4 by autoactivation and clustering drives centriole biogenesis.
Authors: Park, J.E. / Zhang, L. / Bang, J.K. / Andresson, T. / DiMaio, F. / Lee, K.S.
History
DepositionNov 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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: Chimera protein of Serine/threonine-protein kinase PLK4 and DDB1- and CUL4-associated factor 1
B: Chimera protein of Serine/threonine-protein kinase PLK4 and DDB1- and CUL4-associated factor 1


Theoretical massNumber of molelcules
Total (without water)61,1812
Polymers61,1812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-15 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.659, 61.659, 137.276
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Chimera protein of Serine/threonine-protein kinase PLK4 and DDB1- and CUL4-associated factor 1 / Polo-like kinase 4 / PLK-4 / Serine/threonine-protein kinase 18 / Serine/threonine-protein kinase ...Polo-like kinase 4 / PLK-4 / Serine/threonine-protein kinase 18 / Serine/threonine-protein kinase Sak / HIV-1 Vpr-binding protein / VprBP / Serine/threonine-protein kinase VPRBP / Vpr-interacting protein


Mass: 30590.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK4, SAK, STK18, DCAF1, KIAA0800, RIP, VPRBP / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: O00444, UniProt: Q9Y4B6, polo kinase, non-specific serine/threonine protein kinase

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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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 4.3M Ammonium Acetate 0.1M BisTris propane pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 17096 / % possible obs: 99.9 % / Redundancy: 11.7 % / Net I/σ(I): 49.7
Reflection shellResolution: 2.64→2.73 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 2.8 / CC1/2: 0.886 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000715.5data collection
HKL-2000715.5data reduction
HKL-2000715.5data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N9J

4n9j


Resolution: 2.64→34.77 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.873 / SU B: 27.42 / SU ML: 0.262 / Cross valid method: FREE R-VALUE / ESU R: 0.509 / ESU R Free: 0.359 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31396 838 4.9 %RANDOM
Rwork0.234 ---
obs0.23803 16254 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 82.374 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0.65 Å20 Å2
2---1.29 Å20 Å2
3---4.19 Å2
Refinement stepCycle: 1 / Resolution: 2.64→34.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 0 0 2933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133004
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172549
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.6474110
X-RAY DIFFRACTIONr_angle_other_deg1.3491.5695845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1175398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5522.358123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.33415383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6431512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023438
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02626
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.2578.2581622
X-RAY DIFFRACTIONr_mcbond_other6.2538.2571620
X-RAY DIFFRACTIONr_mcangle_it8.74212.3762010
X-RAY DIFFRACTIONr_mcangle_other8.73512.3762010
X-RAY DIFFRACTIONr_scbond_it5.948.2311382
X-RAY DIFFRACTIONr_scbond_other5.9398.2311383
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.22212.2882101
X-RAY DIFFRACTIONr_long_range_B_refined11.20399.4313256
X-RAY DIFFRACTIONr_long_range_B_other11.20199.4363257
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.641→2.709 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 63 -
Rwork0.245 1173 -
obs--100 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-13.599646.1815-41.815
2-13.936851.9089-45.6047
3-19.223828.2993-27.2951
4-14.735117.3562-33.0782
5-22.66059.4835-36.0425
6-27.61728.2797-24.7372
7-21.953539.485-21.3198
8-13.411425.23644.2693
9-13.225316.107510.5064
10-14.111431.25326.7633
11-17.831743.8499-8.3872
12-15.961754.145-0.3795
13-23.749460.70122.454
14-25.576740.4859-12.0643
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A586 - 632
2X-RAY DIFFRACTION2A633 - 699
3X-RAY DIFFRACTION3A700 - 725
4X-RAY DIFFRACTION4A726 - 751
5X-RAY DIFFRACTION5A752 - 765
6X-RAY DIFFRACTION6A766 - 793
7X-RAY DIFFRACTION7A794 - 804
8X-RAY DIFFRACTION8B588 - 624
9X-RAY DIFFRACTION9B633 - 686
10X-RAY DIFFRACTION10B687 - 696
11X-RAY DIFFRACTION11B697 - 731
12X-RAY DIFFRACTION12B732 - 751
13X-RAY DIFFRACTION13B752 - 763
14X-RAY DIFFRACTION14B764 - 804

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