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- PDB-6mf6: Crystal structure of budding yeast Cdc5 polo-box domain in comple... -

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Basic information

Entry
Database: PDB / ID: 6mf6
TitleCrystal structure of budding yeast Cdc5 polo-box domain in complex with the Dbf4 polo-interacting region.
Components
  • Cell cycle serine/threonine-protein kinase CDC5/MSD2
  • DDK kinase regulatory subunit DBF4
KeywordsCELL CYCLE / Transferase / Mitosis / Dbf4 / Polo-like kinases
Function / homology
Function and homology information


positive regulation of mitotic spindle pole body separation / positive regulation of protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / regulation of protein localization to mitotic spindle pole body / regulation of nucleus organization / Polo-like kinase mediated events / Regulation of PLK1 Activity at G2/M Transition / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Golgi Cisternae Pericentriolar Stack Reorganization / negative regulation of protein localization to nucleolus / positive regulation of kinetochore assembly ...positive regulation of mitotic spindle pole body separation / positive regulation of protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / regulation of protein localization to mitotic spindle pole body / regulation of nucleus organization / Polo-like kinase mediated events / Regulation of PLK1 Activity at G2/M Transition / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Golgi Cisternae Pericentriolar Stack Reorganization / negative regulation of protein localization to nucleolus / positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / positive regulation of DNA replication initiation / negative regulation of exit from mitosis / Resolution of Sister Chromatid Cohesion / Dbf4-dependent protein kinase complex / meiotic spindle assembly / regulation of protein localization to nucleolus / positive regulation of meiosis I / positive regulation of nuclear cell cycle DNA replication / regulation of cell cycle phase transition / mitotic spindle pole body / synaptonemal complex disassembly / polo kinase / centromeric DNA binding / resolution of meiotic recombination intermediates / premeiotic DNA replication / Activation of the pre-replicative complex / cellular bud neck / exit from mitosis / Activation of ATR in response to replication stress / mitotic DNA replication checkpoint signaling / spindle pole body / positive regulation of Rho protein signal transduction / DNA replication origin binding / chromosome, centromeric region / DNA replication initiation / protein serine/threonine kinase activator activity / mitotic spindle organization / chromosome segregation / phosphoprotein binding / kinetochore / G2/M transition of mitotic cell cycle / spindle pole / protein kinase activity / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / chromatin / zinc ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Regulatory subunit Dfp1/Him1, central region / : / Dfp1/Him1, central region / BRCT domain / Zinc finger, DBF-type / DBF-type zinc finger superfamily / : / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins ...Regulatory subunit Dfp1/Him1, central region / : / Dfp1/Him1, central region / BRCT domain / Zinc finger, DBF-type / DBF-type zinc finger superfamily / : / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / BRCT 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
DDK kinase regulatory subunit DBF4 / Cell cycle serine/threonine-protein kinase CDC5/MSD2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsGuarne, A. / Almawi, A.W.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Sci Rep / Year: 2020
Title: Distinct surfaces on Cdc5/PLK Polo-box domain orchestrate combinatorial substrate recognition during cell division.
Authors: Almawi, A.W. / Langlois-Lemay, L. / Boulton, S. / Rodriguez Gonzalez, J. / Melacini, G. / D'Amours, D. / Guarne, A.
History
DepositionSep 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell cycle serine/threonine-protein kinase CDC5/MSD2
B: Cell cycle serine/threonine-protein kinase CDC5/MSD2
D: DDK kinase regulatory subunit DBF4
C: DDK kinase regulatory subunit DBF4


Theoretical massNumber of molelcules
Total (without water)71,4194
Polymers71,4194
Non-polymers00
Water00
1
A: Cell cycle serine/threonine-protein kinase CDC5/MSD2
C: DDK kinase regulatory subunit DBF4


Theoretical massNumber of molelcules
Total (without water)35,7102
Polymers35,7102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-5 kcal/mol
Surface area13390 Å2
MethodPISA
2
B: Cell cycle serine/threonine-protein kinase CDC5/MSD2
D: DDK kinase regulatory subunit DBF4


Theoretical massNumber of molelcules
Total (without water)35,7102
Polymers35,7102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-5 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.054, 135.054, 75.163
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Cell cycle serine/threonine-protein kinase CDC5/MSD2


Mass: 33463.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CDC5, MSD2, PKX2, YMR001C, YM8270.03C / Production host: Escherichia coli (E. coli) / References: UniProt: P32562, polo kinase
#2: Protein/peptide DDK kinase regulatory subunit DBF4 / Dumbbell forming protein 4


Mass: 2246.552 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: DBF4, DNA52, YDR052C, D4205, YD9609.07C / Production host: Escherichia coli (E. coli) / References: UniProt: P32325

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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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium potassium tartrate, 10 mM trimethylamine hydrochloride, 20 % PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.4→67.5 Å / Num. obs: 10923 / % possible obs: 100 % / Redundancy: 18.9 % / CC1/2: 0.998 / Net I/σ(I): 10.92
Reflection shellResolution: 3.4→3.49 Å / CC1/2: 0.315

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q4O

1q4o


Resolution: 3.4→44.207 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.283 553 5.09 %
Rwork0.2433 --
obs0.2454 10856 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→44.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3701 0 0 0 3701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043799
X-RAY DIFFRACTIONf_angle_d0.7115180
X-RAY DIFFRACTIONf_dihedral_angle_d11.0761262
X-RAY DIFFRACTIONf_chiral_restr0.031600
X-RAY DIFFRACTIONf_plane_restr0.003660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4003-3.74240.44841260.41712577X-RAY DIFFRACTION100
3.7424-4.28350.3871420.36092548X-RAY DIFFRACTION99
4.2835-5.39520.32741330.26612564X-RAY DIFFRACTION99
5.3952-44.21050.21411520.17822614X-RAY DIFFRACTION100
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)
10.08440.1861-0.1012-0.2862-0.0120.13160.69230.1694-2.4805-0.35050.3291-1.52860.8481.57550.00312.9337-0.4938-0.25851.7660.08231.937378.2211-17.49237.8636
23.02020.26092.8813-0.1670.5302-0.98390.05130.6071-0.5949-0.39491.3034-0.2840.29111.81810.11782.99180.09030.08640.9015-0.18281.429468.8133-13.1621-10.4571
31.86870.69392.51620.8547-0.65052.63780.8167-1.0903-0.0142-0.5674-1.95721.8549-1.4532-0.9976-0.20582.25510.7122-0.00291.3146-0.04171.404947.7972-15.6387-4.9658
40.7997-0.21670.40730.2678-0.43041.8227-1.4854-0.10320.9116-1.1253-1.73751.64080.0724-1.2307-2.77271.37853.36720.0115-0.0377-1.03742.16940.7779-12.1993-13.5529
53.899-0.5657-0.82681.7722-0.47240.8901-0.08411.4104-1.16650.4690.16091.2985-2.9568-0.35040.9582.69661.0411-0.12872.42980.14511.769545.4152-20.5305-17.6429
6-0.01890.17070.46320.41180.80161.20190.0510.128-0.8975-0.82950.284-0.665-1.0168-0.9903-0.00142.30310.4555-0.09142.17180.15981.835242.4629-21.7204-20.3315
70.0272-0.12010.07150.16830.0617-0.0305-1.36380.1983-0.2495-1.6995-0.7080.78991.5886-2.8128-0.00142.40230.1996-0.08772.8197-0.1862.363136.5828-19.206-4.7751
80.0985-0.02460.03520.02430.08570.2432.10272.0083-1.16150.2277-0.2110.8616-0.0415-0.46-0.00183.96540.98590.92852.90180.14953.31138.7138-6.58324.849
90.64920.45090.22830.1830.04720.01221.06010.93492.613-0.045-2.7769-1.08230.2495-1.3468-0.01983.26121.1354-0.58141.9034-0.27072.183450.5031-9.3062-17.7191
109.77791.16421.33270.188-0.02720.9919-0.3692-2.30692.391-0.47030.2338-0.7763-1.4117-0.66150.23262.34160.43120.10120.84390.05562.077756.4347-20.0245-5.2718
115.1821.708-0.2910.5956-0.30930.55190.9155-0.9283-1.3888-0.67880.44561.5009-0.7718-0.38880.21242.53070.5354-0.29660.86620.00161.569459.8957-14.0566-2.9412
12-0.1560.0557-0.2882-0.01460.15240.08770.09821.5993-0.3379-0.57460.95471.2463-0.0161-1.6467-0.01162.98950.4017-0.08421.25550.1541.750462.3164-6.6055-1.4184
134.67051.95175.20331.06722.24375.80841.9329-2.23890.35522.31110.2117-2.19661.7608-3.32960.59883.63790.72160.39671.7319-0.03151.883158.1189-0.85790.4343
140.8224-0.3532-0.19720.5594-0.5250.3621-0.5681-0.89772.8536-0.10731.35920.3354-1.0591-0.03030.014.39350.2732-0.07081.4822-0.31381.964867.4851.83440.7554
153.0802-0.6676-0.70560.12520.02640.3257-0.1649-2.4581-0.59170.5274-0.9921-1.1183-0.92791.6005-0.17073.1544-0.1468-0.26540.89960.37021.692570.205-13.2469-0.0505
160.27330.0236-0.21090.08550.1070.0461-0.2738-1.1128-0.81120.1586-0.34530.6525-0.48460.81870.00133.1669-0.0424-0.26091.31480.09561.917166.5149-29.0255-10.0783
171.9773-2.35190.81563.6739-1.30051.28361.473-1.04261.1368-2.80490.0065-1.2810.82780.73150.1171.3704-0.26060.17112.0462-0.00112.401262.6962-35.529411.7215
180.06290.04780.20130.0862-0.2152.3099-0.38290.851-0.38620.6759-2.8493-1.0078-0.36580.0537-0.00023.6392-0.3998-0.30851.6707-0.09051.397957.8103-19.410424.1867
190.983-1.10430.39420.59980.22370.2578-0.61570.21620.03620.21531.5859-2.28340.29190.12410.03541.9907-0.9454-0.30181.94170.31171.911455.9933-40.973625.8378
200.08340.60320.09024.20270.51110.05831.7974-0.1024-1.42820.94121.2465-3.1360.8194-0.02170.52392.7613-1.70290.53562.5936-0.49490.193446.1517-59.465425.9671
210.0066-0.02190.05790.5769-0.09750.07680.21042.2246-2.20731.67510.48080.78910.72960.4235-0.00582.2563-0.71550.3851.9319-0.33471.560540.6719-53.168328.7762
220.8811-0.4015-1.45990.1248-0.22050.52570.8257-0.89120.5270.0061-1.31970.9487-1.1455-0.11520.00281.77490.23260.23011.70120.09831.595441.7992-29.062314.1428
230.664-0.82340.03761.0354-0.15030.27751.15830.83170.6059-1.3832-1.27951.4659-1.22680.13950.00022.29280.64740.66312.48860.04621.960639.2726-20.708619.1437
241.07320.40880.09734.2777-1.26720.21651.2582-1.6569-2.97693.1641-4.0859-2.99370.6975-3.9161-0.0913.79010.37840.74393.92560.05332.368140.3475-17.031527.1461
25-0.2617-0.18550.22761.2127-0.80160.50772.83881.8122.4374-0.4419-2.817-1.5708-0.9339-1.53930.00113.07750.60020.15222.8862-0.02552.045841.1855-15.085530.1136
261.04750.5931-0.9160.684-0.40970.5093-0.42820.08760.54650.43690.5241-0.06671.6236-3.00580.00052.9585-0.3586-0.05843.02920.02772.227536.0406-14.395512.2261
270.27560.0742-0.44070.2647-0.32460.96911.93461.1799-0.4892-0.2734-1.68982.0681-0.47071.23011.15072.85650.0940.66672.8765-0.18561.841936.9731-28.710428.2314
280.04010.0623-0.2125-0.05490.10690.1716-0.381-0.64271.4537-1.67861.6542-3.3598-0.19750.153-0.00162.4512-0.4283-0.06011.87360.05441.320951.5549-26.603318.5136
29-0.0319-0.384-0.12850.6798-0.11940.33630.490.29520.81030.4395-0.5282-1.1309-1.4326-1.8213-01.5069-0.21130.18462.012-0.15821.403750.2353-33.330815.4236
30-0.13350.24470.0211.10940.1118-0.0505-1.1318-1.49151.36420.12042.02981.43990.0038-3.34580.02071.6495-0.41280.36282.48890.13861.288646.0274-38.91579.1539
311.4363-1.5667-0.47073.0242-1.45321.8087-1.62090.2147-0.70710.68111.2090.6709-0.3536-2.2431-0.36270.3646-0.6414-0.16583.00210.10041.320341.8934-41.763215.4817
324.02810.6617-4.18942.46671.14397.40863.49990.5946-1.85593.5968-1.31671.3204-2.0513-3.46953.06561.4142-1.7465-0.61112.8097-0.51.458643.5937-50.782317.1463
330.11490.0620.03920.1146-0.13380.10420.11021.3042-0.78620.19660.54150.2202-0.8706-0.7492-0.00082.3628-0.6755-0.27432.8573-0.06351.681344.8259-49.5877.3131
341.0428-0.80180.06470.37730.28580.4696-0.3569-0.0703-1.07360.34370.5069-1.42640.91051.69670.00261.6743-0.67030.22581.6610.05171.678257.2581-41.038315.0089
350.01230.08280.03260.1796-0.05330.05610.92060.16151.42691.2340.35590.31190.18730.0323-0.00612.3601-0.33440.3192.1474-0.58632.708365.1762-24.563323.8741
365.2385-6.06564.21219.7225-6.14793.976-0.930.20071.6197-0.55890.2462-2.14170.35082.2466-2.41632.532-0.07320.41411.2943-0.2621.080839.6619-24.076833.7194
373.4887-6.0698-0.88262.04890.31592.2026-2.2441-0.13891.70962.17290.1803-3.35931.35883.9191-0.82383.7750.57610.25831.88930.13981.330750.1285-13.8906-22.4799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 451 through 460 )
2X-RAY DIFFRACTION2chain 'A' and (resid 461 through 507 )
3X-RAY DIFFRACTION3chain 'A' and (resid 508 through 543 )
4X-RAY DIFFRACTION4chain 'A' and (resid 544 through 552 )
5X-RAY DIFFRACTION5chain 'A' and (resid 553 through 560 )
6X-RAY DIFFRACTION6chain 'A' and (resid 561 through 579 )
7X-RAY DIFFRACTION7chain 'A' and (resid 580 through 593 )
8X-RAY DIFFRACTION8chain 'A' and (resid 594 through 597 )
9X-RAY DIFFRACTION9chain 'A' and (resid 609 through 614 )
10X-RAY DIFFRACTION10chain 'A' and (resid 615 through 620 )
11X-RAY DIFFRACTION11chain 'A' and (resid 621 through 638 )
12X-RAY DIFFRACTION12chain 'A' and (resid 639 through 651 )
13X-RAY DIFFRACTION13chain 'A' and (resid 652 through 661 )
14X-RAY DIFFRACTION14chain 'A' and (resid 662 through 683 )
15X-RAY DIFFRACTION15chain 'A' and (resid 684 through 698 )
16X-RAY DIFFRACTION16chain 'A' and (resid 699 through 705 )
17X-RAY DIFFRACTION17chain 'B' and (resid 452 through 466 )
18X-RAY DIFFRACTION18chain 'B' and (resid 467 through 470 )
19X-RAY DIFFRACTION19chain 'B' and (resid 471 through 497 )
20X-RAY DIFFRACTION20chain 'B' and (resid 498 through 502 )
21X-RAY DIFFRACTION21chain 'B' and (resid 503 through 507 )
22X-RAY DIFFRACTION22chain 'B' and (resid 508 through 521 )
23X-RAY DIFFRACTION23chain 'B' and (resid 526 through 552 )
24X-RAY DIFFRACTION24chain 'B' and (resid 553 through 559 )
25X-RAY DIFFRACTION25chain 'B' and (resid 560 through 576 )
26X-RAY DIFFRACTION26chain 'B' and (resid 577 through 597 )
27X-RAY DIFFRACTION27chain 'B' and (resid 609 through 614 )
28X-RAY DIFFRACTION28chain 'B' and (resid 615 through 620 )
29X-RAY DIFFRACTION29chain 'B' and (resid 621 through 638 )
30X-RAY DIFFRACTION30chain 'B' and (resid 639 through 646 )
31X-RAY DIFFRACTION31chain 'B' and (resid 647 through 660 )
32X-RAY DIFFRACTION32chain 'B' and (resid 661 through 673 )
33X-RAY DIFFRACTION33chain 'B' and (resid 674 through 683 )
34X-RAY DIFFRACTION34chain 'B' and (resid 684 through 699 )
35X-RAY DIFFRACTION35chain 'B' and (resid 700 through 705 )
36X-RAY DIFFRACTION36chain 'D' and (resid 82 through 91 )
37X-RAY DIFFRACTION37chain 'C' and (resid 83 through 90 )

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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