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- PDB-6w38: Crystal structure of the FAM46C/Plk4 complex -

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Basic information

Entry
Database: PDB / ID: 6w38
TitleCrystal structure of the FAM46C/Plk4 complex
Components
  • Serine/threonine-protein kinase PLK4
  • Terminal nucleotidyltransferase 5C
KeywordsTRANSFERASE / RNA polymerase
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 / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity ...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 / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA stabilization / centriole replication / cleavage furrow / negative regulation of cell differentiation / cilium assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / centriole / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / in utero embryonic development / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Terminal nucleotidyltransferase / Nucleotidyltransferase / Domain of unknown function (DUF1693) / 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. ...Terminal nucleotidyltransferase / Nucleotidyltransferase / Domain of unknown function (DUF1693) / 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. / 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
Similarity search - Domain/homology
Serine/threonine-protein kinase PLK4 / Terminal nucleotidyltransferase 5C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.48 Å
AuthorsChen, H. / Lu, D.F. / Shang, G.J. / Zhang, X.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R01CA220283 United States
Robert A. Welch Foundationi-1702 United States
CitationJournal: Structure / Year: 2020
Title: Structural and Functional Analyses of the FAM46C/Plk4 Complex.
Authors: Chen, H. / Lu, D. / Shang, G. / Gao, G. / Zhang, X.
History
DepositionMar 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 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: Terminal nucleotidyltransferase 5C
B: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)65,9052
Polymers65,9052
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-2 kcal/mol
Surface area30520 Å2
Unit cell
Length a, b, c (Å)87.392, 158.613, 165.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Terminal nucleotidyltransferase 5C / Non-canonical poly(A) polymerase FAM46C


Mass: 40035.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TENT5C, FAM46C / Production host: Escherichia coli (E. coli)
References: UniProt: Q5VWP2, polynucleotide adenylyltransferase
#2: Protein Serine/threonine-protein kinase PLK4 / Polo-like kinase 4 / PLK-4 / Serine/threonine-protein kinase 18 / Serine/threonine-protein kinase Sak


Mass: 25869.609 Da / Num. of mol.: 1 / Fragment: UNP residues 585-807
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: 4.36 Å3/Da / Density % sol: 71.8 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 10 / Details: 0.2 M Tris, pH 10

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 4.48→50 Å / Num. obs: 6713 / % possible obs: 94 % / Redundancy: 6.2 % / Rpim(I) all: 0.025 / Net I/σ(I): 22.2
Reflection shellResolution: 4.5→4.58 Å / Num. unique obs: 271 / CC1/2: 0.847

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4N7Z

4n7z


Resolution: 4.48→46.649 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 30.37
RfactorNum. reflection% reflection
Rfree0.2955 609 9.97 %
Rwork0.232 --
obs0.2381 6111 85.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.48→46.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 0 0 4423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044512
X-RAY DIFFRACTIONf_angle_d1.1856105
X-RAY DIFFRACTIONf_dihedral_angle_d7.3312747
X-RAY DIFFRACTIONf_chiral_restr0.062693
X-RAY DIFFRACTIONf_plane_restr0.009782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.4881-4.93930.31541000.2309920X-RAY DIFFRACTION58
4.9393-5.6530.29911440.24741337X-RAY DIFFRACTION84
5.653-7.11810.3091810.291595X-RAY DIFFRACTION100
7.1181-46.6490.27641840.19361650X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1221-0.38820.43351.76940.09212.14790.01820.2573-0.8602-0.5602-0.0876-0.0446-0.1718-0.31130.04860.59450.14590.12970.1759-0.0350.603126.6013177.9701206.4189
23.9478-1.1329-0.73742.14291.63054.1344-0.0807-0.96110.5102-0.24940.3821-0.4945-0.44710.6311-0.30630.3336-0.0660.09430.89550.23240.658328.6786186.9929235.2483
31.58810.67890.06172.761.431.91360.1651-0.681-0.04690.664-0.1909-0.34960.50180.75780.09590.4733-0.03420.02641.4265-0.01970.357510.0765180.6701259.7424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 12:343 )A12 - 343
2X-RAY DIFFRACTION2( CHAIN B AND RESID 586:700 )B586 - 700
3X-RAY DIFFRACTION3( CHAIN B AND RESID 701:807 )B701 - 807

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