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- PDB-6n46: Crystal structure of the cryptic polo box domain of a human activ... -

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Basic information

Entry
Database: PDB / ID: 6n46
TitleCrystal structure of the cryptic polo box domain of a human activated Plk4
ComponentsSerine/threonine-protein kinase PLK4
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 / 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
Arylsulfatase, C-terminal domain - #120 / Arylsulfatase, C-terminal domain - #130 / 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 ...Arylsulfatase, C-terminal domain - #120 / Arylsulfatase, C-terminal domain - #130 / 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. / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.708 Å
AuthorsPark, J.-E. / DiMaio, F. / Zhang, 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: Serine/threonine-protein kinase PLK4
B: Serine/threonine-protein kinase PLK4
C: Serine/threonine-protein kinase PLK4
D: Serine/threonine-protein kinase PLK4
E: Serine/threonine-protein kinase PLK4
F: Serine/threonine-protein kinase PLK4
G: Serine/threonine-protein kinase PLK4
H: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)230,5428
Polymers230,5428
Non-polymers00
Water00
1
A: Serine/threonine-protein kinase PLK4
B: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)57,6362
Polymers57,6362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-16 kcal/mol
Surface area25760 Å2
MethodPISA
2
C: Serine/threonine-protein kinase PLK4
D: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)57,6362
Polymers57,6362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-14 kcal/mol
Surface area25440 Å2
MethodPISA
3
E: Serine/threonine-protein kinase PLK4
F: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)57,6362
Polymers57,6362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-15 kcal/mol
Surface area25390 Å2
MethodPISA
4
G: Serine/threonine-protein kinase PLK4
H: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)57,6362
Polymers57,6362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-16 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.831, 110.831, 205.682
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
Serine/threonine-protein kinase PLK4 / Polo-like kinase 4 / PLK-4 / Serine/threonine-protein kinase 18 / Serine/threonine-protein kinase Sak


Mass: 28817.754 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK4, SAK, STK18 / Production host: Escherichia coli (E. coli) / References: UniProt: O00444, polo 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: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 22.5% (w/v) PEG2000 3% (w/v) dextran sulfate sodium salt 0.1M bicine (pH 8.5) 24 uM nonaethylene glycol monododecyl ether (C12E9) 8% (w/v) glycerol

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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: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 29891 / % possible obs: 100 % / Redundancy: 11 % / Net I/σ(I): 23.75
Reflection shellResolution: 3.7→3.83 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 2 / CC1/2: 0.838 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3235refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N9J

4n9j


Resolution: 3.708→37.81 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 36.24
RfactorNum. reflection% reflection
Rfree0.309 1987 6.68 %
Rwork0.2709 --
obs0.2734 29747 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.708→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14008 0 0 0 14008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514320
X-RAY DIFFRACTIONf_angle_d0.86819320
X-RAY DIFFRACTIONf_dihedral_angle_d10.7958864
X-RAY DIFFRACTIONf_chiral_restr0.0562080
X-RAY DIFFRACTIONf_plane_restr0.0052472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7079-3.80060.40071440.33961984X-RAY DIFFRACTION99
3.8006-3.90320.37261460.33261957X-RAY DIFFRACTION100
3.9032-4.0180.32121440.2942009X-RAY DIFFRACTION100
4.018-4.14750.32911340.2891981X-RAY DIFFRACTION100
4.1475-4.29560.35781460.29651991X-RAY DIFFRACTION100
4.2956-4.46730.30461410.28352021X-RAY DIFFRACTION100
4.4673-4.67020.34331380.26021993X-RAY DIFFRACTION100
4.6702-4.9160.28951480.26981965X-RAY DIFFRACTION100
4.916-5.22320.3181330.29042029X-RAY DIFFRACTION100
5.2232-5.62530.38791350.29841992X-RAY DIFFRACTION100
5.6253-6.18920.37381510.3041995X-RAY DIFFRACTION100
6.1892-7.07970.33451460.29291982X-RAY DIFFRACTION100
7.0797-8.90040.34771440.25031992X-RAY DIFFRACTION100
8.9004-37.81210.21151370.22681869X-RAY DIFFRACTION94

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