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- PDB-8s31: Crystal structure of human PLK1 Polo-Box Domain in complex with M... -

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Basic information

Entry
Database: PDB / ID: 8s31
TitleCrystal structure of human PLK1 Polo-Box Domain in complex with Mis18BP1
Components
  • Mis18-binding protein 1
  • Serine/threonine-protein kinase PLK1
KeywordsCELL CYCLE / PLK1 / Mis18 complex / Centromere / Chromosome mis segregation
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 / regulation of protein binding / Activation of NIMA Kinases NEK9, NEK6, NEK7 / nuclear membrane disassembly / homologous chromosome segregation / polo kinase ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / regulation of protein binding / Activation of NIMA Kinases NEK9, NEK6, NEK7 / nuclear membrane disassembly / homologous chromosome segregation / polo kinase / mitotic nuclear membrane disassembly / Phosphorylation of Emi1 / protein localization to nuclear envelope / metaphase/anaphase transition of mitotic cell cycle / double-strand break repair via alternative nonhomologous end joining / synaptonemal complex / female meiosis chromosome segregation / anaphase-promoting complex binding / Phosphorylation of the APC/C / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of mitotic spindle assembly / positive regulation of ubiquitin protein ligase activity / microtubule bundle formation / mitotic chromosome condensation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / centrosome cycle / regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin-protein transferase activity / sister chromatid cohesion / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / establishment of mitotic spindle orientation / positive regulation of proteolysis / mitotic sister chromatid segregation / mitotic cytokinesis / centriolar satellite / chromosome, centromeric region / negative regulation of double-strand break repair via homologous recombination / spindle midzone / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / protein localization to chromatin / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / centriole / AURKA Activation by TPX2 / mitotic spindle organization / Condensation of Prophase Chromosomes / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / RHO GTPases Activate Formins / protein destabilization / establishment of protein localization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / kinetochore / spindle pole / positive regulation of protein localization to nucleus / spindle / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / 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 / peptidyl-serine phosphorylation / microtubule binding / regulation of cell cycle / protein kinase activity / protein ubiquitination / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / chromatin / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / DNA binding / nucleoplasm / ATP binding / identical protein binding
Similarity search - Function
SANT associated / KNL2-like / SANTA (SANT Associated) / 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. ...SANT associated / KNL2-like / SANTA (SANT Associated) / 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. / SANT domain profile. / SANT domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / 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 / Mis18-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.134 Å
AuthorsJeyaprakash, A.A. / Medina-Pritchard, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/X001245/1 United Kingdom
CitationJournal: Science / Year: 2024
Title: PLK1-mediated phosphorylation cascade activates Mis18 complex to ensure centromere inheritance.
Authors: Parashara, P. / Medina-Pritchard, B. / Abad, M.A. / Sotelo-Parrilla, P. / Thamkachy, R. / Grundei, D. / Zou, J. / Spanos, C. / Kumar, C.N. / Basquin, C. / Das, V. / Yan, Z. / Al-Murtadha, A. ...Authors: Parashara, P. / Medina-Pritchard, B. / Abad, M.A. / Sotelo-Parrilla, P. / Thamkachy, R. / Grundei, D. / Zou, J. / Spanos, C. / Kumar, C.N. / Basquin, C. / Das, V. / Yan, Z. / Al-Murtadha, A.A. / Kelly, D.A. / McHugh, T. / Imhof, A. / Rappsilber, J. / Jeyaprakash, A.A.
History
DepositionFeb 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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: Mis18-binding protein 1
D: Mis18-binding protein 1


Theoretical massNumber of molelcules
Total (without water)58,5414
Polymers58,5414
Non-polymers00
Water3,801211
1
A: Serine/threonine-protein kinase PLK1
C: Mis18-binding protein 1


Theoretical massNumber of molelcules
Total (without water)29,2702
Polymers29,2702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase PLK1
D: Mis18-binding protein 1


Theoretical massNumber of molelcules
Total (without water)29,2702
Polymers29,2702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.147, 67.147, 254.536
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 368 through 419 or (resid 420...
d_2ens_1(chain "B" and ((resid 368 and (name N or name...
d_1ens_2(chain "C" and ((resid -1 and (name N or name...
d_2ens_2(chain "D" and resid -1 through 6)

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLUGLUARGARGAA368 - 5947 - 233
d_2ens_1GLUGLUARGARGBB368 - 5947 - 233
d_1ens_2ASNASNLEULEUCC-1 - 62 - 9
d_2ens_2ASNASNLEULEUDD-1 - 62 - 9

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.495154516332, -0.367964035532, 0.787035242864), (-0.868691981409, 0.195078362065, -0.455322604413), (0.0140087969236, -0.909146248526, -0.416241339129)-23.0712447928, 71.2820976234, 43.9921980179
2given(-0.48170970082, -0.387364381181, 0.786069081143), (-0.87627691578, 0.202964923765, -0.436971402489), (0.00972270579094, -0.899307553573, -0.437208637928)-22.7967299496, 70.4233508413, 44.5986090602

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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: 27877.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Plasmid: pEC-A-HT-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold / References: UniProt: P53350, polo kinase
#2: Protein/peptide Mis18-binding protein 1 / Kinetochore-associated protein KNL-2 homolog / HsKNL-2 / P243


Mass: 1392.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6P0N0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 50 mM MES (pH 6.0), 20 mM Sodium Oxalate, 1.2 M Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.67021 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.67021 Å / Relative weight: 1
ReflectionResolution: 2.134→29.08 Å / Num. obs: 37897 / % possible obs: 99.16 % / Redundancy: 10 % / Biso Wilson estimate: 34.68 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1043 / Rrim(I) all: 0.1101 / Net I/σ(I): 15.79
Reflection shellResolution: 2.134→2.211 Å / Rmerge(I) obs: 0.7229 / Mean I/σ(I) obs: 2.85 / Num. unique obs: 3442 / CC1/2: 0.799 / CC star: 0.942 / Rpim(I) all: 0.2468 / Rrim(I) all: 0.7656 / % possible all: 92.13

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.134→29.08 Å / SU ML: 0.2227 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2535
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2244 2001 5.28 %
Rwork0.195 35891 -
obs0.1967 37892 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.06 Å2
Refinement stepCycle: LAST / Resolution: 2.134→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 0 0 211 4013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093878
X-RAY DIFFRACTIONf_angle_d1.26585250
X-RAY DIFFRACTIONf_chiral_restr0.0608588
X-RAY DIFFRACTIONf_plane_restr0.0083664
X-RAY DIFFRACTIONf_dihedral_angle_d10.0337532
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.724823897365
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS0.599180022857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.134-2.190.30191260.2372255X-RAY DIFFRACTION89.01
2.19-2.250.25851430.20792544X-RAY DIFFRACTION100
2.25-2.310.26031450.22372567X-RAY DIFFRACTION100
2.31-2.390.22831350.21782514X-RAY DIFFRACTION100
2.39-2.470.24341430.22492541X-RAY DIFFRACTION100
2.47-2.570.28491410.21612565X-RAY DIFFRACTION100
2.57-2.690.25381420.2312552X-RAY DIFFRACTION100
2.69-2.830.26641460.22192542X-RAY DIFFRACTION100
2.83-3.010.26011390.22492566X-RAY DIFFRACTION100
3.01-3.240.23411420.20642585X-RAY DIFFRACTION100
3.24-3.570.21811480.19342592X-RAY DIFFRACTION99.96
3.57-4.080.20261450.16692603X-RAY DIFFRACTION100
4.08-5.140.18571480.15492668X-RAY DIFFRACTION100
5.14-29.080.19951580.19342797X-RAY DIFFRACTION99.83
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)
12.472745409631.142057785591.30114996141.232352549990.2065387986411.596680051560.0783420600560.126879221939-0.4257455903170.04047858929690.0851576113437-0.1095128737960.2169114453690.04062533361-0.1981964564510.2985840251010.02583359245770.02566148233850.219307894374-0.04772814324180.314680733425-0.38909734866217.755437359138.8889178534
28.04197377525-0.99805072132-1.626761627134.419730034670.6751658502445.80172368396-0.0219105137728-0.1365047749970.05344864613240.001804038967210.0562384852243-0.0120928764097-0.24255204034-0.0809150445187-0.01305326646080.2186911723040.00206731945799-0.03039734797250.156942678612-0.01712157773960.17070967436310.194062976234.495581576148.5806723421
33.379417439081.218064597841.264298269331.618041223870.7115706441232.228318882770.07790072304550.254671831249-0.393519452234-0.06785736780260.138455490785-0.2255289024340.3039957492170.178116081819-0.2147070627980.312360711150.01526450451070.01156642195990.21319230129-0.03609534324980.27891897142-1.1894126407215.164400950136.7388029932
42.5050248730.07089611594191.74445180241.53435795682-0.001925624472583.03301760461-0.0830435515495-0.216985762284-0.05260946977750.1391563213150.07821044098770.108812451667-0.270243061633-0.1976859313370.01354687932420.440995938585-0.08669172589340.008379036041080.2803227855220.005601820470410.2882608744824.1746099588968.190857713522.5303806648
50.297524688746-0.718221192187-0.04389468582083.303017412732.117929728682.528194463410.0254421351767-0.023969669867-0.2407174495730.04248177010920.0994538761025-0.01197548975590.1829588292710.0928580230345-0.1136109649090.37740867813-0.139065685317-0.01767819741270.316948933437-0.02105649632160.347519369434-1.2599949134148.76026395842.76546124965
65.39488627143-5.844977540081.124115302486.73595480938-1.845348454453.442405221470.1507118296420.3502490725120.69061574116-0.642509092209-0.0509152005219-0.479111328431-0.02919624825450.198402370509-0.1151838962380.589197715617-0.1992331070870.08723278899710.3676443135050.03437659988260.326123974755-0.44616640061952.4028280845-10.5528257705
75.653169793430.30416209092-1.858252348916.105365087621.13679668235.757843715790.1172853557250.146705037015-0.3428638086640.0964211768176-0.0490500460104-0.1001126131420.189320051752-0.3044729538760.07812339684280.331314180269-0.132807544869-0.03618018105230.2477755992070.007087336947870.318789816783-5.467138192641.4142461776-4.01636919151
80.2621738561760.7506762055380.4592659538128.09003781155-0.04702966997931.117441058890.09716567796250.259828806937-0.01397501880760.436861495902-0.1962243635171.105730977890.0745389766296-0.79737191185-0.0125108777410.405023486396-0.180027736790.06139272133260.3940788286040.05015209738970.395660934305-12.276626206855.24984474410.9354549586
90.638232029979-1.455171524560.684835904265.64234497088-0.252801674661.78943135707-0.2861144439620.194742161031-0.0549888168827-0.274727692960.2806801431190.588869211929-0.183710096397-0.321233204210.04432955193280.446355233225-0.1842466850920.01124526066120.345769348785-0.03965843356640.417234412611-2.3098897368765.0929006486-0.436440815104
103.27114425967-0.4602629878090.1588805643734.026895850151.539662202023.055176205540.0145341796398-0.154105296734-0.08565679660440.3638842209320.08238334585120.137495002630.277074782044-0.150104892433-0.08757319978690.347716899153-0.13762489419-0.003872284006820.234924733473-0.004037721548360.2326517785370.68582826372554.738988418114.8148837292
114.86245528459-1.89268219071-0.3357824300123.255643572381.056100103533.648707307340.0432008263372-0.175452653129-0.03126785822470.2370210629980.0398421536666-0.005696232659990.0937466243434-0.195645433438-0.1283072947340.388847090946-0.117741392215-0.01412419168430.267949394505-0.02913812753390.2737496415825.0178905018262.114097319120.6500084747
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 373 through 444 )AA373 - 4446 - 77
22chain 'A' and (resid 445 through 489 )AA445 - 48978 - 122
33chain 'A' and (resid 490 through 594 )AA490 - 594123 - 227
44chain 'B' and (resid 373 through 405 )BB373 - 4056 - 38
55chain 'B' and (resid 406 through 444 )BB406 - 44439 - 77
66chain 'B' and (resid 445 through 469 )BB445 - 46978 - 102
77chain 'B' and (resid 470 through 489 )BB470 - 489103 - 122
88chain 'B' and (resid 490 through 499 )BB490 - 499123 - 132
99chain 'B' and (resid 500 through 510 )BB500 - 510133 - 143
1010chain 'B' and (resid 511 through 558 )BB511 - 558144 - 191
1111chain 'B' and (resid 559 through 594 )BB559 - 594192 - 227

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