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- PDB-7rl3: Structure of Drosophila melanogaster Plk4 PB3 -

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Basic information

Entry
Database: PDB / ID: 7rl3
TitleStructure of Drosophila melanogaster Plk4 PB3
ComponentsSerine/threonine-protein kinase PLK4
KeywordsSIGNALING PROTEIN / TRANSFERASE / Kinase / Sak Kinase / Plk4 / Polo Box
Function / homology
Function and homology information


syncytial blastoderm mitotic cell cycle / regulation of centriole replication / sperm axoneme assembly / polo kinase / male meiotic nuclear division / centrosome cycle / centriole replication / centriole / mitotic spindle organization / regulation of protein stability ...syncytial blastoderm mitotic cell cycle / regulation of centriole replication / sperm axoneme assembly / polo kinase / male meiotic nuclear division / centrosome cycle / centriole replication / centriole / mitotic spindle organization / regulation of protein stability / kinetochore / spindle pole / positive regulation of protein catabolic process / protein autophosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ATP binding / identical protein binding / nucleus / cytoplasm
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 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
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsSlep, K.C. / Slevin, L.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)5R03HD064881 United States
CitationJournal: Mol.Biol.Cell / Year: 2023
Title: Polo-like kinase 4 homodimerization and condensate formation regulate its own protein levels but are not required for centriole assembly.
Authors: Ryniawec, J.M. / Buster, D.W. / Slevin, L.K. / Boese, C.J. / Amoiroglou, A. / Dean, S.M. / Slep, K.C. / Rogers, G.C.
History
DepositionJul 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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


Theoretical massNumber of molelcules
Total (without water)19,8652
Polymers19,8652
Non-polymers00
Water2,126118
1
A: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)9,9321
Polymers9,9321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)9,9321
Polymers9,9321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.711, 53.095, 41.637
Angle α, β, γ (deg.)90.000, 107.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase PLK4 / Polo-like kinase 4 / PLK-4 / Serine/threonine-protein kinase SAK


Mass: 9932.314 Da / Num. of mol.: 2 / Fragment: Polo Box Domain
Source method: isolated from a genetically manipulated source
Details: native N-terminal cloning artifact: GSHM / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: SAK, CG7186 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: O97143, polo kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.82 Å3/Da / Density % sol: 32.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: D.m. Plk4 PB3 was crystallized using a mother liquor (1 ml) containing 32% PEG 4000, 200 mM Li2SO4, and 200 mM Tris at pH 8.5. The hanging drop initial condition was 2 ul mother liquor plus ...Details: D.m. Plk4 PB3 was crystallized using a mother liquor (1 ml) containing 32% PEG 4000, 200 mM Li2SO4, and 200 mM Tris at pH 8.5. The hanging drop initial condition was 2 ul mother liquor plus 2 ul (15 mg/ml stock) Plk4 PB3. Crystals were transferred to a cryo condition containing mother liquor plus 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 7, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 14468 / % possible obs: 93.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 19.84 Å2 / Rmerge(I) obs: 0.048 / Χ2: 1.033 / Net I/σ(I): 20.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.75-1.812.40.2519611.099162.4
1.81-1.892.70.19511891.007178.8
1.89-1.973.30.14114581.14193.5
1.97-2.073.70.10615311.077199.9
2.07-2.23.70.07815421.0331100
2.2-2.383.50.06715381.045199.9
2.38-2.613.70.06315540.93199.9
2.61-2.993.70.05515430.97199.9
2.99-3.773.70.04115671.054199.7
3.77-503.60.03515851.028199.6

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Processing

Software
NameVersionClassification
PHENIXv1.8refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXv1.8phasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→39.617 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 1420 10.01 %
Rwork0.1922 12766 -
obs0.1964 14186 91.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.51 Å2 / Biso mean: 32.5538 Å2 / Biso min: 17.22 Å2
Refinement stepCycle: final / Resolution: 1.75→39.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1247 0 0 118 1365
Biso mean---42.86 -
Num. residues----165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131273
X-RAY DIFFRACTIONf_angle_d1.6441731
X-RAY DIFFRACTIONf_chiral_restr0.099203
X-RAY DIFFRACTIONf_plane_restr0.009225
X-RAY DIFFRACTIONf_dihedral_angle_d15.478474
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.75-1.80980.2757800.218674653
1.8098-1.88230.27691130.2214101674
1.8823-1.9680.25961430.1985126290
1.968-2.07170.24271520.1902137098
2.0717-2.20150.21421520.1832137699
2.2015-2.37150.2171540.1873137399
2.3715-2.61010.23851560.2026139899
2.6101-2.98760.2581540.20381385100
2.9876-3.76360.22871570.18211413100
3.7636-39.6170.21821590.18931427100
Refinement TLS params.Method: refined / Origin x: 6.4029 Å / Origin y: -6.2661 Å / Origin z: 24.7053 Å
111213212223313233
T0.1771 Å20.0185 Å20.0148 Å2-0.1855 Å2-0.0287 Å2--0.1998 Å2
L0.4323 °2-0.2792 °20.6171 °2-1.1588 °2-0.8911 °2--1.9362 °2
S-0.0512 Å °-0.0173 Å °0.0287 Å °0.0828 Å °0.0608 Å °-0.0093 Å °-0.0886 Å °-0.081 Å °-0.0128 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA660 - 745
2X-RAY DIFFRACTION1allB660 - 743
3X-RAY DIFFRACTION1allS1 - 118

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