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- PDB-4x9r: PLK-1 polo-box domain in complex with Bioactive Imidazolium-conta... -

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Basic information

Entry
Database: PDB / ID: 4x9r
TitlePLK-1 polo-box domain in complex with Bioactive Imidazolium-containing phosphopeptide macrocycle 3B
Components
  • Phosphopeptide macrocycle 3B
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / POLO BOX DOMAIN PHOSPHOPEPTIDE MACROCYCLE INHIBITOR COMPLEX / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 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 / 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 / POLO box domain / POLO box domain profile. / Arylsulfatase, C-terminal domain / 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: 1.398 Å
AuthorsGrant, R.A. / Qian, W.-J. / Yaffe, M.B. / Burke, T.R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES015339 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM68762 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
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 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: Phosphopeptide macrocycle 3B


Theoretical massNumber of molelcules
Total (without water)28,2472
Polymers28,2472
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-8 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.813, 50.979, 57.590
Angle α, β, γ (deg.)90.00, 100.24, 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 Phosphopeptide macrocycle 3B / 1-(1-methylethyl)-1H-benzimidazole-2-sulfonic acid


Mass: 962.101 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.: 189 / 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 Å3/Da / Density % sol: 38.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / 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: 1.398→50 Å / Num. obs: 42019 / % possible obs: 98.4 % / Redundancy: 6.5 % / Rsym value: 0.064 / Net I/σ(I): 3.1
Reflection shellResolution: 1.398→1.42 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.5 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIXdev_1951refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RQ7

3rq7


Resolution: 1.398→37.901 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1789 2000 4.76 %random
Rwork0.1493 ---
obs0.1507 42002 98.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.398→37.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 67 189 2014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121982
X-RAY DIFFRACTIONf_angle_d1.4722708
X-RAY DIFFRACTIONf_dihedral_angle_d12.598797
X-RAY DIFFRACTIONf_chiral_restr0.089302
X-RAY DIFFRACTIONf_plane_restr0.007359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.398-1.43290.21671380.15582757X-RAY DIFFRACTION96
1.4329-1.47160.23111410.14812813X-RAY DIFFRACTION97
1.4716-1.51490.18911420.13672855X-RAY DIFFRACTION98
1.5149-1.56380.20381410.12352811X-RAY DIFFRACTION98
1.5638-1.61970.1821430.12252863X-RAY DIFFRACTION98
1.6197-1.68460.18261420.12542851X-RAY DIFFRACTION99
1.6846-1.76120.18041440.12162879X-RAY DIFFRACTION99
1.7612-1.85410.1881420.12872823X-RAY DIFFRACTION98
1.8541-1.97030.1951440.13292901X-RAY DIFFRACTION99
1.9703-2.12240.18621450.1342878X-RAY DIFFRACTION99
2.1224-2.33590.1541440.13422903X-RAY DIFFRACTION100
2.3359-2.67390.17881420.152823X-RAY DIFFRACTION97
2.6739-3.36850.16881460.16862916X-RAY DIFFRACTION100
3.3685-37.91510.17781460.16482929X-RAY DIFFRACTION98

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