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- PDB-4j7b: Crystal structure of polo-like kinase 1 -

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Basic information

Entry
Database: PDB / ID: 4j7b
TitleCrystal structure of polo-like kinase 1
Components
  • (Polo-like kinase) x 2
  • 205 kDa microtubule-associated protein
KeywordsTRANSFERASE / First complex structure of KD and PBD domain / regulator of mitosis / phosphorylated target protein
Function / homology
Function and homology information


: / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / Phosphorylation of Emi1 / Condensation of Prophase Chromosomes / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / Mitotic Metaphase/Anaphase Transition / Mitotic Telophase/Cytokinesis / Cyclin A/B1/B2 associated events during G2/M transition ...: / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / Phosphorylation of Emi1 / Condensation of Prophase Chromosomes / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / Mitotic Metaphase/Anaphase Transition / Mitotic Telophase/Cytokinesis / Cyclin A/B1/B2 associated events during G2/M transition / EML4 and NUDC in mitotic spindle formation / : / : / : / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / : / : / : / : / Anchoring of the basal body to the plasma membrane / : / polo kinase / centrosome cycle / microtubule associated complex / mitotic spindle organization / spindle / kinetochore / spindle pole / retina development in camera-type eye / mitotic cell cycle / midbody / microtubule / cell division / phosphorylation / protein serine/threonine kinase activity / centrosome / ATP binding / nucleus / cytoplasm
Similarity search - Function
POLO box domain / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Arylsulfatase, C-terminal domain / Transferase(Phosphotransferase) domain 1 ...POLO box domain / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Arylsulfatase, C-terminal domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
205 kDa microtubule-associated protein / Serine/threonine-protein kinase PLK
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXu, J. / Shen, C. / Quan, J. / Wang, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structural basis for the inhibition of Polo-like kinase 1
Authors: Xu, J. / Shen, C. / Wang, T. / Quan, J.
History
DepositionFeb 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Jun 8, 2016Group: Derived calculations
Revision 1.3Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polo-like kinase
B: Polo-like kinase
C: 205 kDa microtubule-associated protein
D: Polo-like kinase
E: Polo-like kinase
F: 205 kDa microtubule-associated protein


Theoretical massNumber of molelcules
Total (without water)135,9996
Polymers135,9996
Non-polymers00
Water6,485360
1
A: Polo-like kinase
B: Polo-like kinase
C: 205 kDa microtubule-associated protein


Theoretical massNumber of molelcules
Total (without water)67,9993
Polymers67,9993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-25 kcal/mol
Surface area26080 Å2
MethodPISA
2
D: Polo-like kinase
E: Polo-like kinase
F: 205 kDa microtubule-associated protein


Theoretical massNumber of molelcules
Total (without water)67,9993
Polymers67,9993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-25 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.681, 57.453, 125.736
Angle α, β, γ (deg.)89.150, 89.840, 72.380
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22D
13B
23E
14B
24E
15C
25F
/ NCS ensembles :
ID
1
2
3
4
5
DetailsKD:PBD 1:1

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Components

#1: Protein Polo-like kinase / / Uncharacterized protein


Mass: 34106.910 Da / Num. of mol.: 2 / Fragment: Kinase Domain, UNP residues 18-312 / Mutation: D162N, E192F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: plk1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) PLysS / References: UniProt: Q6DRK7, polo kinase
#2: Protein Polo-like kinase / / Uncharacterized protein


Mass: 27206.227 Da / Num. of mol.: 2 / Fragment: Polo Box Domain, UNP residues 360-595 / Mutation: D384G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: plk1 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) PLysS / References: UniProt: Q6DRK7, polo kinase
#3: Protein 205 kDa microtubule-associated protein


Mass: 6686.270 Da / Num. of mol.: 2 / Fragment: UNP residues 276-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Map205, CG1483 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) PLysS / References: UniProt: P23226
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 50mM Bis-Tris, 100mM MOPS, 100mM NaCl, 12.5% PEG3350, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 56677 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.3-2.34194.1
2.38-2.43194.3
2.48-2.53193.4
4.32-4.94196.7
4.94-6.21196.3
6.21-25198.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D5W

3d5w


Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.038 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.398 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 2705 5.1 %RANDOM
Rwork0.2048 ---
obs0.2077 53265 93.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 166.15 Å2 / Biso mean: 51.6355 Å2 / Biso min: 17.13 Å2
Baniso -1Baniso -2Baniso -3
1-4.67 Å2-0.3 Å2-1.56 Å2
2--0.94 Å2-1.97 Å2
3----5.92 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8810 0 0 360 9170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0199005
X-RAY DIFFRACTIONr_bond_other_d0.0010.028688
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.97212150
X-RAY DIFFRACTIONr_angle_other_deg0.864320022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17451079
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69323.095420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.224151633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6851576
X-RAY DIFFRACTIONr_chiral_restr0.0960.21333
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219943
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022073
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2595LOOSE POSITIONAL0.565
1A2595LOOSE THERMAL2.0510
2A1709LOOSE POSITIONAL0.525
2A1709LOOSE THERMAL2.310
3B1756LOOSE POSITIONAL0.485
3B1756LOOSE THERMAL3.2710
4B1514LOOSE POSITIONAL0.455
4B1514LOOSE THERMAL2.4410
5C735LOOSE POSITIONAL0.565
5C735LOOSE THERMAL1.7510
LS refinement shellResolution: 2.3→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 182 -
Rwork0.277 3578 -
all-3760 -
obs--90.58 %
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)
11.5789-0.39510.50214.34450.30623.8051-0.00080.3340.2968-0.6901-0.1261-0.1585-0.33350.03840.12690.2078-0.08080.07870.27840.1590.45495.29135.947-43.912
22.2752.49-0.60355.9554-1.631.7772-0.13510.00230.07750.20590.140.0034-0.0442-0.059-0.00490.07080.02230.06910.08590.09640.36099.68225.841-15.248
34.4330.9723-0.38826.02210.48823.8379-0.1151-0.134-0.3104-0.14510.0152-0.02180.10450.06240.09990.26950.05380.15660.23770.15980.36784.34317.847-2.424
41.63730.46730.2623.36771.02675.0670.2785-0.1364-0.27990.5463-0.5610.09350.4165-0.47570.28250.1885-0.08630.15380.63080.04290.4986-18.24421.96546.229
52.6199-1.58930.9973.3279-1.20473.8431-0.2979-0.34230.04510.06980.11910.0547-0.1657-0.19210.17890.0620.0740.06420.30640.03750.3733-13.78831.34617.607
68.6972-0.35541.1173.76220.18446.1225-0.1845-0.72050.40270.0943-0.04210.0161-0.3804-0.17020.22660.28770.0867-0.04450.28550.06660.4206-19.45639.064.672
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 187
2X-RAY DIFFRACTION1A198 - 311
3X-RAY DIFFRACTION2B363 - 479
4X-RAY DIFFRACTION2B490 - 585
5X-RAY DIFFRACTION3C276 - 324
6X-RAY DIFFRACTION4D20 - 187
7X-RAY DIFFRACTION4D199 - 311
8X-RAY DIFFRACTION5E363 - 479
9X-RAY DIFFRACTION5E490 - 585
10X-RAY DIFFRACTION6F276 - 324

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