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- PDB-2v5q: CRYSTAL STRUCTURE OF WILD-TYPE PLK-1 KINASE DOMAIN IN COMPLEX WIT... -

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Basic information

Entry
Database: PDB / ID: 2v5q
TitleCRYSTAL STRUCTURE OF WILD-TYPE PLK-1 KINASE DOMAIN IN COMPLEX WITH A SELECTIVE DARPIN
Components
  • DESIGN ANKYRIN REPEAT PROTEIN
  • SERINE/THREONINE-PROTEIN KINASE PLK1
KeywordsTRANSFERASE / DESIGN ANKYRIN REPEAT PROTEIN / TRANSFERASE COMPLEX / PHOSPHORYLATION / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / KINASE / NUCLEUS / ATP-BINDING / SERINE/THREONINE PROTEIN KINASE
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / mitotic nuclear membrane disassembly / polo kinase / protein localization to nuclear envelope ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / mitotic nuclear membrane disassembly / polo kinase / protein localization to nuclear envelope / Phosphorylation of Emi1 / nuclear membrane disassembly / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / Phosphorylation of the APC/C / anaphase-promoting complex binding / outer kinetochore / positive regulation of ubiquitin protein ligase activity / double-strand break repair via alternative nonhomologous end joining / microtubule bundle formation / mitotic chromosome condensation / Polo-like kinase mediated events / regulation of mitotic spindle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / centrosome cycle / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / regulation of mitotic cell cycle phase transition / positive regulation of ubiquitin-protein transferase activity / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / mitotic G2 DNA damage checkpoint signaling / regulation of anaphase-promoting complex-dependent catabolic process / establishment of mitotic spindle orientation / positive regulation of proteolysis / mitotic cytokinesis / mitotic sister chromatid segregation / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin A/B1/B2 associated events during G2/M transition / protein localization to chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / 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 / Resolution of Sister Chromatid Cohesion / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / AURKA Activation by TPX2 / regulation of cytokinesis / mitotic spindle organization / RHO GTPases Activate Formins / establishment of protein localization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / protein destabilization / kinetochore / positive regulation of protein localization to nucleus / centriolar satellite / spindle / spindle pole / G2/M transition of mitotic cell cycle / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / mitotic cell cycle / peptidyl-serine phosphorylation / microtubule cytoskeleton / midbody / microtubule binding / protein kinase activity / regulation of cell cycle / protein ubiquitination / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / negative regulation of apoptotic process / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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. / Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...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. / Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBandeiras, T.M. / Hillig, R.C. / Matias, P.M. / Eberspaecher, U. / Fanghaenel, J. / Thomaz, M. / Miranda, S. / Crusius, K. / Puetter, V. / Amstutz, P. ...Bandeiras, T.M. / Hillig, R.C. / Matias, P.M. / Eberspaecher, U. / Fanghaenel, J. / Thomaz, M. / Miranda, S. / Crusius, K. / Puetter, V. / Amstutz, P. / Gulotti-Georgieva, M. / Binz, H.K. / Holz, C. / Schmitz, A.A.P. / Lang, C. / Donner, P. / Egner, U. / Carrondo, M.A. / Mueller-Tiemann, B.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2008
Title: Structure of wild-type Plk-1 kinase domain in complex with a selective DARPin.
Authors: Bandeiras, T.M. / Hillig, R.C. / Matias, P.M. / Eberspaecher, U. / Fanghanel, J. / Thomaz, M. / Miranda, S. / Crusius, K. / Putter, V. / Amstutz, P. / Gulotti-Georgieva, M. / Binz, H.K. / ...Authors: Bandeiras, T.M. / Hillig, R.C. / Matias, P.M. / Eberspaecher, U. / Fanghanel, J. / Thomaz, M. / Miranda, S. / Crusius, K. / Putter, V. / Amstutz, P. / Gulotti-Georgieva, M. / Binz, H.K. / Holz, C. / Schmitz, A.A. / Lang, C. / Donner, P. / Egner, U. / Carrondo, M.A. / Muller-Tiemann, B.
History
DepositionJul 8, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 20, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _citation_author.name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE PLK1
B: SERINE/THREONINE-PROTEIN KINASE PLK1
C: DESIGN ANKYRIN REPEAT PROTEIN
D: DESIGN ANKYRIN REPEAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)107,6184
Polymers107,6184
Non-polymers00
Water7,314406
1
A: SERINE/THREONINE-PROTEIN KINASE PLK1
D: DESIGN ANKYRIN REPEAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,8092
Polymers53,8092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-5.7 kcal/mol
Surface area22410 Å2
MethodPQS
2
B: SERINE/THREONINE-PROTEIN KINASE PLK1
C: DESIGN ANKYRIN REPEAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,8092
Polymers53,8092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-5.5 kcal/mol
Surface area23400 Å2
MethodPQS
Unit cell
Length a, b, c (Å)62.329, 135.225, 136.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE PLK1 / PLK-1 / SERINE/THREONINE-PROTEIN KINASE 13 / STPK13 / POLO-LIKE KINASE 1 / HUMAN POLO-LIKE KINASE 1


Mass: 35972.875 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 33-345
Source method: isolated from a genetically manipulated source
Details: CONSTRUCT 4 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53350, polo kinase
#2: Protein DESIGN ANKYRIN REPEAT PROTEIN


Mass: 17835.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: VARIANT 3H10 / Source: (gene. exp.) synthetic construct (others) / Description: DESIGNED PROTEIN / Production host: ESCHERICHIA COLI (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 303 K
Details: 0.1 M TRIS-HCL PH 8.0, 8% PEG 5000 MME, 0.01 M EDTA SODIUM SALT AT 303 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.037
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 20, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.037 Å / Relative weight: 1
ReflectionResolution: 2.3→96.2 Å / Num. obs: 51702 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.3 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
PHASER1.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PLK-1 - HOMOLOGY MODEL FROM PDB ENTRY 1OL5 DARPIN 3H10 - PDB ENTRY 1MJ0 TRUNCATED AFTER RESIDUE 141

1ol5

3h10

1mj0


Resolution: 2.3→61.08 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.227 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2601 5 %RANDOM
Rwork0.182 ---
obs0.184 49051 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2---1.87 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→61.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6502 0 0 406 6908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226697
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.989072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9525833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47723.49298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.116151188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8751549
X-RAY DIFFRACTIONr_chiral_restr0.0870.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025019
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.23169
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24572
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2453
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.61534262
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.866691
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.21492691
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.068122377
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.287 172
Rwork0.226 3580
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)
15.6756-2.297-3.54163.0215-1.1855.9214-0.0418-0.3611-0.18780.48110.25480.9448-0.4088-0.5455-0.213-0.12410.0763-0.02160.0725-0.02250.1671-14.7929.12533.139
21.52730.06440.22013.13990.132.1696-0.0387-0.14070.1577-0.08750.0795-0.2592-0.20760.0773-0.0407-0.22670.08520.0149-0.156-0.0615-0.220610.06732.41428.827
38.827-5.307-2.41149.49921.18871.4472-0.1891-0.3782-0.755-0.08320.1317-0.51040.39840.57040.0574-0.11030.11180.03080.19530.020.119130.653-1.57710.71
42.40060.6165-0.32712.719-0.56712.639-0.10860.141-0.1117-0.4210.1813-0.176-0.16580.0279-0.0726-0.11830.03850.1146-0.2196-0.0192-0.197611.46812.1322.141
52.73950.7043-0.23743.18280.84094.1490.05570.0616-0.3610.0332-0.10630.07270.1993-0.28280.0506-0.18030.016-0.016-0.22750.0711-0.0968-1.958-13.71417.794
61.43940.20420.24237.07081.42343.81780.1239-0.4054-0.17281.20070.1309-0.49750.49830.0303-0.25470.12690.0837-0.1111-0.03240.0678-0.15416.4917.31150.362
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 131
2X-RAY DIFFRACTION2A132 - 323
3X-RAY DIFFRACTION3B45 - 131
4X-RAY DIFFRACTION4B132 - 323
5X-RAY DIFFRACTION5C13 - 141
6X-RAY DIFFRACTION6D14 - 141

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