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- PDB-4x9w: PLK-1 polo-box domain in complex with Bioactive Imidazolium-conta... -

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Basic information

Entry
Database: PDB / ID: 4x9w
TitlePLK-1 polo-box domain in complex with Bioactive Imidazolium-containing phosphopeptide macrocycle 4C
Components
  • Macrocyclic phosphopeptide 4C
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / positive regulation of mitotic nuclear envelope disassembly / Mitotic Metaphase/Anaphase Transition / Activation of NIMA Kinases NEK9, NEK6, NEK7 / polo kinase / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / mitotic nuclear membrane disassembly / anaphase-promoting complex binding ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / positive regulation of mitotic nuclear envelope disassembly / Mitotic Metaphase/Anaphase Transition / Activation of NIMA Kinases NEK9, NEK6, NEK7 / polo kinase / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / mitotic nuclear membrane disassembly / anaphase-promoting complex binding / Phosphorylation of the APC/C / synaptonemal complex / Golgi inheritance / astral microtubule organization / mitotic cleavage furrow formation / outer kinetochore / microtubule bundle formation / mitotic chromosome condensation / double-strand break repair via alternative nonhomologous end joining / regulation of mitotic spindle assembly / Polo-like kinase mediated events / positive regulation of mitotic metaphase/anaphase transition / Golgi Cisternae Pericentriolar Stack Reorganization / centrosome cycle / positive regulation of ubiquitin-dependent protein catabolic process / sister chromatid cohesion / regulation of mitotic metaphase/anaphase transition / centriolar satellite / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / regulation of mitotic cell cycle phase transition / spindle midzone / mitotic G2 DNA damage checkpoint signaling / regulation of anaphase-promoting complex-dependent catabolic process / mitotic sister chromatid segregation / mitotic cytokinesis / 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 / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Recruitment of mitotic centrosome proteins and complexes / centriole / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / regulation of mitotic cell cycle / regulation of cytokinesis / Condensation of Prophase Chromosomes / establishment of protein localization / G2/M transition of mitotic cell cycle / RHO GTPases Activate Formins / positive regulation of protein localization to nucleus / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / spindle / kinetochore / spindle pole / microtubule cytoskeleton / double-strand break repair / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / midbody / microtubule binding / regulation of cell cycle / protein kinase activity / 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 box domain / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / Arylsulfatase, C-terminal domain / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site ...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 / Arylsulfatase, C-terminal domain / POLO box domain / POLO box domain profile. / 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 / 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: 1.798 Å
AuthorsGrant, R.A. / Qian, W.-J. / Yaffe, M.B. / Burke, T.R.
CitationJournal: Biopolymers / Year: 2015
Title: Neighbor-directed histidine N ( tau )-alkylation: A route to imidazolium-containing phosphopeptide macrocycles.
Authors: Qian, W.J. / Park, J.E. / Grant, R. / Lai, C.C. / Kelley, J.A. / Yaffe, M.B. / Lee, K.S. / Burke, T.R.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references / Source and taxonomy
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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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: Macrocyclic phosphopeptide 4C


Theoretical massNumber of molelcules
Total (without water)28,1942
Polymers28,1942
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-7 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.052, 51.525, 57.449
Angle α, β, γ (deg.)90.00, 100.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase PLK1 / Polo-like kinase 1 / PLK-1 / Serine/threonine-protein kinase 13 / STPK13


Mass: 27285.158 Da / Num. of mol.: 1 / Fragment: POLO box domain residues 371-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Production host: Escherichia coli (E. coli) / References: UniProt: P53350, polo kinase
#2: Protein/peptide Macrocyclic phosphopeptide 4C / (4aS)-5-[(2 / 4-diaminopteridin-6-yl)methyl]-4a / 5-dihydro-2H-dibenzo[b / f]azepin-8-ol


Mass: 909.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.92 Å3/Da / Density % sol: 36.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8
Details: Frozen stocks of protein at 37 mg/mL in 10 mM TRIS pH8, 0.5 M NaCl, 10 mM DTT were thawed and diluted to 10 mg/ml with the same buffer. Complexes with each of three macrocycle compounds (3b, ...Details: Frozen stocks of protein at 37 mg/mL in 10 mM TRIS pH8, 0.5 M NaCl, 10 mM DTT were thawed and diluted to 10 mg/ml with the same buffer. Complexes with each of three macrocycle compounds (3b, 3c and 4b) were prepared by adding 100 mM stocks of the macrocycle in DMSO directly to the diluted protein to achieve a final concentration of 1 mM. Crystals were grown by hanging drop vapor diffusion, with drops made by mixing equal volumes of protein-macrocycle complex and well solution containing 2-6% PEG-3350. Crystals were cryo-protected by quickly dipping in a solution of 37.5% ethylene glycol in well solution and frozen in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.798→100 Å / Num. obs: 18528 / % possible obs: 95.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 27.05 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Χ2: 1.153 / Net I/av σ(I): 32.875 / Net I/σ(I): 7 / Num. measured all: 117363
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.798-1.835.40.3017530.9650.1320.3290.88280.2
1.83-1.865.60.2728310.9720.1160.2970.88186.9
1.86-1.95.70.2469110.9790.1030.2670.89192
1.9-1.945.90.2118880.9840.0890.2290.87294.3
1.94-1.986.10.1969460.9820.0830.2130.95496.3
1.98-2.036.10.1849050.9850.0780.20.95996.4
2.03-2.086.10.169400.9890.0670.1741.00597.2
2.08-2.136.10.1469560.9890.0620.1581.0696.4
2.13-2.260.1258770.9910.0530.1361.05594.7
2.2-2.276.70.1179570.9950.0480.1271.03797.8
2.27-2.356.80.1179370.9920.0480.1271.08798.5
2.35-2.446.80.1059660.9950.0430.1140.97898.5
2.44-2.556.70.0999480.9930.0410.1071.06298.4
2.55-2.696.60.0829460.9960.0340.0891.03797.2
2.69-2.866.20.0749320.9950.0320.0811.11895.9
2.86-3.0870.0699550.9970.0280.0751.25598.8
3.08-3.396.80.069580.9970.0250.0651.37799.2
3.39-3.886.60.0559750.9970.0230.061.51998.8
3.88-4.896.50.0539560.9980.0220.0581.897.6
4.89-1006.60.0589910.9960.0240.0631.82197.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1951)refinement
HKL-2000(phenix.refine: dev_1951)data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RQ7

3rq7


Resolution: 1.798→38.065 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 1850 10 %random
Rwork0.1944 ---
obs0.1987 18493 95.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.798→38.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 62 73 1966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042031
X-RAY DIFFRACTIONf_angle_d0.8462764
X-RAY DIFFRACTIONf_dihedral_angle_d12.639816
X-RAY DIFFRACTIONf_chiral_restr0.041305
X-RAY DIFFRACTIONf_plane_restr0.003362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.798-1.84650.34511180.25741065X-RAY DIFFRACTION81
1.8465-1.90090.32171360.25271211X-RAY DIFFRACTION91
1.9009-1.96220.28391390.22761256X-RAY DIFFRACTION95
1.9622-2.03240.26551440.21451294X-RAY DIFFRACTION97
2.0324-2.11370.24991420.20581284X-RAY DIFFRACTION96
2.1137-2.20990.23881410.19241265X-RAY DIFFRACTION95
2.2099-2.32640.28711450.19861315X-RAY DIFFRACTION98
2.3264-2.47210.24321470.20551315X-RAY DIFFRACTION98
2.4721-2.6630.22861450.19321311X-RAY DIFFRACTION98
2.663-2.93090.23071440.20391298X-RAY DIFFRACTION97
2.9309-3.35470.25721500.19841342X-RAY DIFFRACTION99
3.3547-4.22580.22121460.17791323X-RAY DIFFRACTION98
4.2258-38.07320.21431530.18241364X-RAY DIFFRACTION98

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