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- PDB-7mso: Crystal Structure of Polo Box Domain in Complex with Cyclic Pepti... -

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Basic information

Entry
Database: PDB / ID: 7mso
TitleCrystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor
Components
  • Cyclic Peptide Inhibitor ZO1-GLN-SER-TPO-45W-MLL
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE/Inhibitor / phosphopeptide binding domain / TRANSFERASE-Inhibitor complex
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / homologous chromosome segregation / protein localization to nuclear envelope / polo kinase ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / homologous chromosome segregation / protein localization to nuclear envelope / polo kinase / nuclear membrane disassembly / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / Phosphorylation of the APC/C / anaphase-promoting complex binding / regulation of protein binding / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / double-strand break repair via alternative nonhomologous end joining / positive regulation of ubiquitin protein ligase activity / regulation of mitotic spindle assembly / microtubule bundle formation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / mitotic chromosome condensation / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / positive regulation of ubiquitin-protein transferase activity / centrosome cycle / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic sister chromatid segregation / mitotic G2 DNA damage checkpoint signaling / positive regulation of proteolysis / establishment of mitotic spindle orientation / mitotic cytokinesis / centriolar satellite / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / regulation of mitotic cell cycle / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / mitotic spindle organization / Condensation of Prophase Chromosomes / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / RHO GTPases Activate Formins / protein destabilization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / establishment of protein localization / kinetochore / spindle / spindle pole / positive regulation of protein localization to nucleus / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / microtubule binding / peptidyl-serine phosphorylation / protein ubiquitination / regulation of cell cycle / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / chromatin / negative regulation of apoptotic process / protein kinase binding / magnesium ion binding / negative regulation of transcription by RNA polymerase II / 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. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase 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. / 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
Similarity search - Domain/homology
: / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsLim, D.C. / Yaffe, M.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R35-ES028374 United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: Novel Macrocyclic Peptidomimetics Targeting the Polo-Box Domain of Polo-Like Kinase 1.
Authors: Ryu, S. / Park, J.E. / Ham, Y.J. / Lim, D.C. / Kwiatkowski, N.P. / Kim, D.H. / Bhunia, D. / Kim, N.D. / Yaffe, M.B. / Son, W. / Kim, N. / Choi, T.I. / Swain, P. / Kim, C.H. / Lee, J.Y. / ...Authors: Ryu, S. / Park, J.E. / Ham, Y.J. / Lim, D.C. / Kwiatkowski, N.P. / Kim, D.H. / Bhunia, D. / Kim, N.D. / Yaffe, M.B. / Son, W. / Kim, N. / Choi, T.I. / Swain, P. / Kim, C.H. / Lee, J.Y. / Gray, N.S. / Lee, K.S. / Sim, T.
History
DepositionMay 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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.pdbx_leaving_atom_flag

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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
E: Cyclic Peptide Inhibitor ZO1-GLN-SER-TPO-45W-MLL
F: Cyclic Peptide Inhibitor ZO1-GLN-SER-TPO-45W-MLL


Theoretical massNumber of molelcules
Total (without water)56,2484
Polymers56,2484
Non-polymers00
Water5,909328
1
A: Serine/threonine-protein kinase PLK1
E: Cyclic Peptide Inhibitor ZO1-GLN-SER-TPO-45W-MLL


Theoretical massNumber of molelcules
Total (without water)28,1242
Polymers28,1242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-7 kcal/mol
Surface area10710 Å2
MethodPISA
2
B: Serine/threonine-protein kinase PLK1
F: Cyclic Peptide Inhibitor ZO1-GLN-SER-TPO-45W-MLL


Theoretical massNumber of molelcules
Total (without water)28,1242
Polymers28,1242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-7 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.282, 64.652, 70.163
Angle α, β, γ (deg.)90.000, 92.490, 90.000
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: P53350, polo kinase
#2: Protein/peptide Cyclic Peptide Inhibitor ZO1-GLN-SER-TPO-45W-MLL


Type: Cyclic peptide / Class: Inhibitor / Mass: 838.762 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002479
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.04 % / Mosaicity: 0.5 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.5 / Details: 0.1 M Bis-Tris pH 5.5, 2.75 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 24, 2009 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→15 Å / Num. obs: 43552 / % possible obs: 99.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 26.22 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1.012 / Net I/σ(I): 19.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.85-1.923.80.3842821.011198.7
1.92-1.993.80.27242861.008198.9
1.99-2.084.10.19343091.005198.9
2.08-2.194.20.14243630.976199.5
2.19-2.334.20.11243541.033199.7
2.33-2.514.20.09943581.042199.9
2.51-2.764.30.0843541.0441100
2.76-3.164.30.0643961.0311100
3.16-3.964.30.04943980.997199.9
3.96-154.20.04644521.025199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FVH

3fvh


Resolution: 1.85→14.83 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 2003 4.6 %
Rwork0.1629 41516 -
obs0.165 43519 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.31 Å2 / Biso mean: 32.3968 Å2 / Biso min: 13.59 Å2
Refinement stepCycle: final / Resolution: 1.85→14.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 0 1634 328 5501
Biso mean--29.84 39.99 -
Num. residues----254
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.90.25661400.20992851299198
1.9-1.950.24741520.19322932308499
1.95-20.25811410.17492931307299
2-2.070.23411360.16452980311699
2.07-2.140.20481480.1482924307299
2.14-2.230.18721470.14932967311499
2.23-2.330.20221280.151729943122100
2.33-2.450.20721430.167129653108100
2.45-2.60.24711450.174629773122100
2.6-2.80.25561410.178929973138100
2.8-3.080.22671510.171929793130100
3.08-3.520.22011410.155929873128100
3.52-4.420.18481450.139530173162100
4.42-14.830.17331450.17473015316099
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)
10.4410.402-0.02091.2549-0.41770.6012-0.28750.3262-0.1129-0.47510.09920.31950.1708-0.1134-0.00460.40660.0341-0.08990.3015-0.03370.2712-13.0616-2.765925.2301
20.11830.130.12340.14440.05850.1553-0.0751-0.5009-0.13160.2680.25960.32970.0442-0.01340.00010.31110.02880.01250.2839-0.03980.3546-14.6031-9.706137.8682
31.305-0.31830.27440.2410.5740.50570.06450.0047-0.13950.04060.0027-0.1440.00990.125500.17830.02160.00930.2060.02450.245513.34290.271440.3746
41.10940.84430.40282.86750.39840.4403-0.30170.1978-1.4359-1.14490.1877-0.40350.4960.2088-0.04850.30920.1237-0.06190.4057-0.07920.561422.5672-6.724432.8198
50.33740.0251-0.12180.00930.01010.0541-0.1431-0.20360.1984-0.0599-0.0308-0.3373-0.0808-0.0652-0.15480.20190.2083-0.01570.78740.15590.64228.9679-5.975844.9586
60.36150.485-0.06750.56530.62450.09430.0355-0.48090.03280.10760.1056-0.2029-0.06220.35970.00220.19480.02070.01320.34950.00150.28219.76464.878746.212
70.0985-0.1087-0.04680.0740.10950.12740.0951-0.11770.0142-0.0062-0.39670.13450.2567-0.1156-0.00060.3057-0.02920.03190.24670.01490.1988-0.0617-2.330448.9942
80.01770.0311-0.00010.04580.00090.0095-0.02020.1523-0.8696-0.0803-0.237-0.55960.043-0.04310.00070.31220.03310.08350.3031-0.01250.507911.3484-9.327135.6977
90.96380.68760.16040.5109-0.46630.5822-0.02920.15340.0671-0.1585-0.05790.01290.05530.1234-0.00040.25320.03920.00070.21230.00450.17463.84274.395832.6549
101.56360.5626-0.29750.4586-0.34560.34830.1212-0.13910.0757-0.0342-0.0796-0.05970.0771-0.02660.00010.23310.0237-0.02280.2325-0.02950.1961-6.24790.814438.4373
111.36120.29640.54191.65210.21280.3973-0.0285-0.06130.1345-0.1089-0.0090.3685-0.01460.00830.00010.28780.025-0.0260.2345-0.00880.2242-10.10680.177830.0842
120.5285-0.4566-0.09740.51970.40210.4547-0.4234-0.20510.20930.33930.272-0.17260.1920.012-0.01350.33980.0324-0.05880.30360.01030.245965.6851-1.08980.1243
130.1242-0.03810.13020.16710.08220.082-0.57220.3063-0.0028-0.66130.3802-0.01830.19660.17180.0010.3133-0.02770.040.27460.04030.335667.2984-8.520168.1476
142.03920.1047-0.47220.5155-0.19630.97250.01860.0017-0.249-0.01670.02610.12110.0703-0.15220.00010.1693-0.0231-0.01260.1881-0.00970.246436.7181-0.21766.0225
150.4925-0.5279-0.24690.5416-0.29540.0013-0.05030.50630.0223-0.13690.13340.1747-0.0229-0.31010.00070.1737-0.007-0.01720.34520.00110.242132.65985.435458.8697
160.09680.0740.01410.0228-0.06240.23560.3453-0.0025-0.0622-0.5433-0.4841-0.07240.23360.14990.00030.28880.0327-0.00340.24430.00140.18652.7239-1.992856.5883
170.3273-0.05830.38320.27670.19470.6603-0.17310.1134-0.17170.05960.46390.50850.6576-0.04520.06810.45-0.0570.00030.2206-0.00630.363143.9492-12.272566.9658
180.9059-0.47010.49290.37020.08160.5345-0.0441-0.21210.00470.0988-0.02190.03440.0511-0.0261-00.2142-0.01730.0070.1972-0.00810.163948.83855.710972.3212
191.6026-0.2430.10610.26010.2970.48920.11380.13610.01230.1093-0.04970.05210.05480.071-0.00010.2164-0.00510.00430.21460.02930.199958.76831.474167.0327
201.465-0.41150.17391.3449-0.29070.5999-0.1053-0.03940.12040.01940.0546-0.2128-0.1052-0.0539-00.2857-0.0019-0.02730.23670.00860.231461.77821.930275.7955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 373 through 396 )A373 - 396
2X-RAY DIFFRACTION2chain 'A' and (resid 397 through 405 )A397 - 405
3X-RAY DIFFRACTION3chain 'A' and (resid 406 through 454 )A406 - 454
4X-RAY DIFFRACTION4chain 'A' and (resid 455 through 464 )A455 - 464
5X-RAY DIFFRACTION5chain 'A' and (resid 465 through 469 )A465 - 469
6X-RAY DIFFRACTION6chain 'A' and (resid 470 through 489 )A470 - 489
7X-RAY DIFFRACTION7chain 'A' and (resid 490 through 499 )A490 - 499
8X-RAY DIFFRACTION8chain 'A' and (resid 506 through 510 )A506 - 510
9X-RAY DIFFRACTION9chain 'A' and (resid 511 through 534 )A511 - 534
10X-RAY DIFFRACTION10chain 'A' and (resid 535 through 558 )A535 - 558
11X-RAY DIFFRACTION11chain 'A' and (resid 559 through 592 )A559 - 592
12X-RAY DIFFRACTION12chain 'B' and (resid 373 through 396 )B373 - 396
13X-RAY DIFFRACTION13chain 'B' and (resid 397 through 405 )B397 - 405
14X-RAY DIFFRACTION14chain 'B' and (resid 406 through 469 )B406 - 469
15X-RAY DIFFRACTION15chain 'B' and (resid 470 through 489 )B470 - 489
16X-RAY DIFFRACTION16chain 'B' and (resid 490 through 499 )B490 - 499
17X-RAY DIFFRACTION17chain 'B' and (resid 501 through 510 )B501 - 510
18X-RAY DIFFRACTION18chain 'B' and (resid 511 through 534 )B511 - 534
19X-RAY DIFFRACTION19chain 'B' and (resid 535 through 558 )B535 - 558
20X-RAY DIFFRACTION20chain 'B' and (resid 559 through 594 )B559 - 594

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