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- PDB-6w3j: Crystal structure of the FAM46C/Plk4/Cep192 complex -

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Basic information

Entry
Database: PDB / ID: 6w3j
TitleCrystal structure of the FAM46C/Plk4/Cep192 complex
Components
  • Centrosomal protein of 192 kDa
  • Serine/threonine-protein kinase PLK4
  • Terminal nucleotidyltransferase 5C
KeywordsTRANSFERASE / RNA polymerase
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 / polynucleotide adenylyltransferase ...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 / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA stabilization / protein localization to centrosome / centrosome cycle / pericentriolar material / centriole replication / cleavage furrow / cilium assembly / negative regulation of cell differentiation / mitotic spindle assembly / phosphatase binding / 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 / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / response to bacterium / 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
Centrosomal protein Spd-2/CEP192 / : / : / : / : / : / Cep192 domain 1 / Cep192 domain 2 / Cep192 domain 7 / Cep192 domain 8 ...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 / 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. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase PLK4 / Terminal nucleotidyltransferase 5C / Centrosomal protein of 192 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.385 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
C: Centrosomal protein of 192 kDa


Theoretical massNumber of molelcules
Total (without water)68,5383
Polymers68,5383
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-14 kcal/mol
Surface area31550 Å2
Unit cell
Length a, b, c (Å)88.033, 161.449, 167.471
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
#3: Protein/peptide Centrosomal protein of 192 kDa / Cep192/SPD-2


Mass: 2632.828 Da / Num. of mol.: 1 / Fragment: UNP residues 217-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP192, KIAA1569, PP8407 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TEP8

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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: 4.34 Å3/Da / Density % sol: 71.67 %
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: Feb 15, 2017
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: 4.38→50 Å / Num. obs: 7771 / % possible obs: 99.1 % / Redundancy: 18.7 % / Rpim(I) all: 0.023 / Net I/σ(I): 26.9
Reflection shellResolution: 4.38→4.48 Å / Num. unique obs: 367 / CC1/2: 0.891

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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: 4.385→37.166 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 31.51
RfactorNum. reflection% reflection
Rfree0.3139 663 9.85 %
Rwork0.2633 --
obs0.2683 6730 84.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.385→37.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 0 0 4608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044702
X-RAY DIFFRACTIONf_angle_d1.0756362
X-RAY DIFFRACTIONf_dihedral_angle_d7.2072856
X-RAY DIFFRACTIONf_chiral_restr0.054718
X-RAY DIFFRACTIONf_plane_restr0.008817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3855-4.72350.342830.2641801X-RAY DIFFRACTION57
4.7235-5.19770.35311200.2741043X-RAY DIFFRACTION74
5.1977-5.94720.35181390.28461296X-RAY DIFFRACTION91
5.9472-7.48270.36711590.30911423X-RAY DIFFRACTION100
7.4827-37.1660.23411620.22331504X-RAY DIFFRACTION100
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)
12.1998-1.00010.56741.1282-0.0620.94320.07410.143-0.6587-0.3501-0.05310.1964-0.091-0.15630.04350.40110.13380.10210.1141-0.03260.354627.0962181.383209.652
23.4774-0.5639-0.87250.87390.52272.46840.3886-0.92551.04140.0801-0.0315-0.3078-0.48810.3615-0.24970.3058-0.13020.17090.7731-0.03640.718527.6704192.2188240.3987
31.03050.1828-0.59310.68020.2780.577-0.0466-0.74940.0210.3332-0.1665-0.0530.32260.6185-0.65280.35960.08860.03211.2316-0.07550.345310.0205184.8418262.9883
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 C AND RESID 217:238 ) OR ( CHAIN B AND RESID 586:700 )C217 - 238
3X-RAY DIFFRACTION2( CHAIN C AND RESID 217:238 ) OR ( CHAIN B AND RESID 586:700 )B586 - 700
4X-RAY DIFFRACTION3( CHAIN B AND RESID 701:807 )B701 - 807

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