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- PDB-4n7z: Crystal structure of human Plk4 cryptic polo box (CPB) in complex... -

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Basic information

Entry
Database: PDB / ID: 4n7z
TitleCrystal structure of human Plk4 cryptic polo box (CPB) in complex with a Cep192 N-terminal fragment
Components
  • Centrosomal protein of 192 kDa
  • Serine/threonine-protein kinase PLK4
KeywordsCELL CYCLE / K/R crater / D-rich motif / Centriole biogenesis / Cep192 / Centrosome
Function / homology
Function and homology information


centrosome-templated microtubule nucleation / 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 / protein localization to centrosome ...centrosome-templated microtubule nucleation / 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 / protein localization to centrosome / pericentriolar material / centriole replication / cleavage furrow / centrosome duplication / cilium assembly / mitotic spindle assembly / phosphatase binding / 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 / response to bacterium / Regulation of PLK1 Activity at G2/M Transition / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / protein kinase binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Centrosomal protein Spd-2/CEP192 / : / : / : / : / : / : / : / : / Cep192 domain 1 ...Centrosomal protein Spd-2/CEP192 / : / : / : / : / : / : / : / : / Cep192 domain 1 / Cep192 domain 2 / Cep192 domain 7 / Cep192 domain 8 / Cep192 domain 3 / Cep192 domain 4 / Cep192 domain 5 / Cep192 domain 6 / 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 / : / 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. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Centrosomal protein 192 / Serine/threonine-protein kinase PLK4 / Centrosomal protein of 192 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPark, S.-Y. / Park, J.-E. / Tian, L. / Kim, T.-S. / Yang, W. / Lee, K.S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Molecular basis for unidirectional scaffold switching of human Plk4 in centriole biogenesis.
Authors: Park, S.Y. / Park, J.E. / Kim, T.S. / Kim, J.H. / Kwak, M.J. / Ku, B. / Tian, L. / Murugan, R.N. / Ahn, M. / Komiya, S. / Hojo, H. / Kim, N.H. / Kim, B.Y. / Bang, J.K. / Erikson, R.L. / Lee, ...Authors: Park, S.Y. / Park, J.E. / Kim, T.S. / Kim, J.H. / Kwak, M.J. / Ku, B. / Tian, L. / Murugan, R.N. / Ahn, M. / Komiya, S. / Hojo, H. / Kim, N.H. / Kim, B.Y. / Bang, J.K. / Erikson, R.L. / Lee, K.W. / Kim, S.J. / Oh, B.H. / Yang, W. / Lee, K.S.
History
DepositionOct 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Sep 20, 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

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK4
B: Centrosomal protein of 192 kDa


Theoretical massNumber of molelcules
Total (without water)33,2432
Polymers33,2432
Non-polymers00
Water81145
1
A: Serine/threonine-protein kinase PLK4
B: Centrosomal protein of 192 kDa

A: Serine/threonine-protein kinase PLK4
B: Centrosomal protein of 192 kDa


Theoretical massNumber of molelcules
Total (without water)66,4854
Polymers66,4854
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area7320 Å2
ΔGint-44 kcal/mol
Surface area26010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.308, 67.308, 287.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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: 26575.330 Da / Num. of mol.: 1 / Fragment: UNP residues 580-808
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
#2: Protein Centrosomal protein of 192 kDa


Mass: 6667.253 Da / Num. of mol.: 1 / Fragment: UNP residues 201-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP192 / Production host: Escherichia coli (E. coli) / References: UniProt: K7ELX0, UniProt: Q8TEP8*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2013
RadiationMonochromator: double crystal - liqued nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 10857 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.115 / Rsym value: 0.09 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.75-2.86.40.8381.655110.79594.3
2.8-2.857.30.7712.335000.78796.7
2.85-2.98.20.5743.135140.58399

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G7N

4g7n


Resolution: 2.85→29.145 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 977 10 %RANDOM
Rwork0.2345 ---
all0.2372 9860 --
obs0.2324 9773 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→29.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 0 45 2078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152079
X-RAY DIFFRACTIONf_angle_d1.4672805
X-RAY DIFFRACTIONf_dihedral_angle_d18.412794
X-RAY DIFFRACTIONf_chiral_restr0.103302
X-RAY DIFFRACTIONf_plane_restr0.008358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.00010.34261330.3251201X-RAY DIFFRACTION100
3.0001-3.18790.32471360.28181222X-RAY DIFFRACTION100
3.1879-3.43370.27751360.25211224X-RAY DIFFRACTION100
3.4337-3.77850.27171380.22751238X-RAY DIFFRACTION100
3.7785-4.32380.26291380.22361243X-RAY DIFFRACTION100
4.3238-5.44170.22261400.20841268X-RAY DIFFRACTION99
5.4417-29.14670.2551560.23651400X-RAY DIFFRACTION100

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