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- PDB-2n19: STIL binding to the Polo-box domain 3 of PLK4 regulates centriole... -

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Basic information

Entry
Database: PDB / ID: 2n19
TitleSTIL binding to the Polo-box domain 3 of PLK4 regulates centriole duplication
ComponentsSerine/threonine-protein kinase PLK4
KeywordsTRANSFERASE
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 / 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)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model1
AuthorsBoehm, R. / Arquint, C. / Gabryjonczyk, A. / Imseng, S. / Sauer, E. / Hiller, S. / Nigg, E. / 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: BMRB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2May 25, 2016Group: Database references
Revision 1.3Dec 28, 2016Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)9,6301
Polymers9,6301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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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: 9629.829 Da / Num. of mol.: 1 / 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 (E. coli) / References: UniProt: O00444, polo kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CA)CB
1513D HN(CA)CO
1623D 1H-15N NOESY
1723D 1H-13C NOESY aliphatic
1833D (H)C(CC)-TOCSY-(CO)-15N-HSQC
1933D H(C)(CC)-TOCSY-(CO)-15N-HSQC
110415N-filtered BPP-LED NMR
111415N-{1H}-Heteronuclear NOE
11232D 1H-13C HSQC aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6-1.2 M [U-13C; U-15N; U-2H] PLK4-PB3, 20 mM MOPS, 30 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O95% H2O/5% D2O
20.6-1.2 M [U-2H,15N,methyl13C/rest-12C-ILV]-PB3 PLK4-PB3, 20 mM MOPS, 30 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O95% H2O/5% D2O
31200 mM [U-2H,15N,13C,methyl13C/1H-ILV]-PB3 PLK4-PB3, 20 mM MOPS, 30 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O95% H2O/5% D2O
4600 mM [U-2H, U-15N] PLK4-PB3, 20 mM MOPS, 30 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
MPLK4-PB3-1[U-13C; U-15N; U-2H]0.6-1.21
20 mMMOPS-21
30 mMsodium chloride-31
2 mMTCEP-41
MPLK4-PB3-5[U-2H,15N,methyl13C/rest-12C-ILV]-PB30.6-1.22
20 mMMOPS-62
30 mMsodium chloride-72
2 mMTCEP-82
1200 mMPLK4-PB3-9[U-2H,15N,13C,methyl13C/1H-ILV]-PB33
20 mMMOPS-103
30 mMsodium chloride-113
2 mMTCEP-123
600 mMPLK4-PB3-13[U-2H, U-15N]4
20 mMMOPS-144
30 mMsodium chloride-154
2 mMTCEP-164
Sample conditionsIonic strength: 0.03 / pH: 7 / Pressure: ambient / Temperature: 293.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichpeak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANArefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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