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- PDB-4y72: Human CDK1/CyclinB1/CKS2 With Inhibitor -

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Basic information

Entry
Database: PDB / ID: 4y72
TitleHuman CDK1/CyclinB1/CKS2 With Inhibitor
Components
  • Cyclin-dependent kinase 1
  • Cyclin-dependent kinases regulatory subunit 2
  • G2/mitotic-specific cyclin-B1
KeywordsTRANSFERASE / CDK1 / CyclinB1 / CKS2 / Inhibitor
Function / homology
Function and homology information


regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / mitotic cell cycle phase transition ...regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / mitotic cell cycle phase transition / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / ventricular cardiac muscle cell development / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / Depolymerization of the Nuclear Lamina / positive regulation of attachment of spindle microtubules to kinetochore / MASTL Facilitates Mitotic Progression / regulation of mitotic cell cycle spindle assembly checkpoint / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / : / cyclin A2-CDK1 complex / Phosphorylation of Emi1 / patched binding / Transcriptional regulation by RUNX2 / Nuclear Pore Complex (NPC) Disassembly / Phosphorylation of the APC/C / outer kinetochore / meiosis I / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / protein localization to kinetochore / RNA polymerase II CTD heptapeptide repeat Y1 kinase activity / RNA polymerase II CTD heptapeptide repeat S2 kinase activity / RNA polymerase II CTD heptapeptide repeat T4 kinase activity / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / RNA polymerase II CTD heptapeptide repeat S7 kinase activity / Initiation of Nuclear Envelope (NE) Reformation / Polo-like kinase mediated events / response to copper ion / cyclin-dependent protein serine/threonine kinase activator activity / Golgi Cisternae Pericentriolar Stack Reorganization / Condensation of Prometaphase Chromosomes / centrosome cycle / chromosome condensation / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / SCF ubiquitin ligase complex / mitotic metaphase chromosome alignment / MAPK3 (ERK1) activation / cyclin-dependent protein kinase activity / response to amine / G1/S-Specific Transcription / mitotic G2 DNA damage checkpoint signaling / microtubule organizing center / : / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin-like protein ligase binding / regulation of embryonic development / protein deubiquitination / response to axon injury / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin A/B1/B2 associated events during G2/M transition / response to cadmium ion / Nuclear events stimulated by ALK signaling in cancer / cyclin-dependent protein kinase holoenzyme complex / positive regulation of cardiac muscle cell proliferation / positive regulation of G2/M transition of mitotic cell cycle / epithelial cell differentiation / RNA polymerase II CTD heptapeptide repeat kinase activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / peptidyl-threonine phosphorylation / ERK1 and ERK2 cascade / Recruitment of mitotic centrosome proteins and complexes / Hsp70 protein binding / APC/C:Cdc20 mediated degradation of Cyclin B / positive regulation of mitotic cell cycle / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / cyclin binding / regulation of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Condensation of Prophase Chromosomes / AURKA Activation by TPX2 / ubiquitin binding / mitotic spindle organization / response to activity / positive regulation of DNA replication / spindle microtubule / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / regulation of circadian rhythm / MAPK6/MAPK4 signaling / PKR-mediated signaling / positive regulation of protein localization to nucleus / microtubule cytoskeleton organization
Similarity search - Function
: / Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / : ...: / Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-LZ9 / Cyclin-dependent kinase 1 / G2/mitotic-specific cyclin-B1 / Cyclin-dependent kinases regulatory subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBrown, N.R. / Korolchuk, S. / Martin, M.P. / Stanley, W. / Moukhametzianov, R. / Noble, M.E.M. / Endicott, J.A.
CitationJournal: Nat Commun / Year: 2015
Title: CDK1 structures reveal conserved and unique features of the essential cell cycle CDK.
Authors: Brown, N.R. / Korolchuk, S. / Martin, M.P. / Stanley, W.A. / Moukhametzianov, R. / Noble, M.E. / Endicott, J.A.
History
DepositionFeb 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: Cyclin-dependent kinase 1
B: G2/mitotic-specific cyclin-B1
C: Cyclin-dependent kinases regulatory subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5754
Polymers76,2143
Non-polymers3601
Water6,630368
1


  • Idetical with deposited unit
  • defined by software
  • TRIMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-19 kcal/mol
Surface area28790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.166, 68.646, 166.771
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cyclin-dependent kinase 1 / CDK1 / Cell division control protein 2 homolog / Cell division protein kinase 1 / p34 protein kinase


Mass: 34553.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK1, CDC2, CDC28A, CDKN1, P34CDC2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P06493, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein G2/mitotic-specific cyclin-B1


Mass: 31369.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNB1, CCNB / Plasmid: PET-28 A+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CODONPLUS RIL / References: UniProt: P14635
#3: Protein Cyclin-dependent kinases regulatory subunit 2 / CKS-2


Mass: 10290.819 Da / Num. of mol.: 1 / Fragment: residues 165-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CKS2 / Plasmid: GST-3C / Production host: Escherichia coli (E. coli) / References: UniProt: P33552
#4: Chemical ChemComp-LZ9 / {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide


Mass: 360.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H11F3N4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.7
Details: Conditions around 0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97957 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.3→53 Å / Num. all: 34085 / Num. obs: 34085 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0103refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1hck, 2b9r, 1jst

1hck

2b9r

1jst


Resolution: 2.3→53 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 1697 5 %RANDOM
Rwork0.1861 32313 --
obs0.1895 34010 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.85 Å2 / Biso mean: 48.7092 Å2 / Biso min: 20.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.68 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.3→53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5139 0 26 368 5533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195310
X-RAY DIFFRACTIONr_bond_other_d00.025155
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9677185
X-RAY DIFFRACTIONr_angle_other_deg3.5682.99711874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58723.75240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04415974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4861532
X-RAY DIFFRACTIONr_chiral_restr0.0870.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215869
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021218
X-RAY DIFFRACTIONr_mcbond_it1.2792.5462529
X-RAY DIFFRACTIONr_mcbond_other1.2792.5442526
X-RAY DIFFRACTIONr_mcangle_it2.2733.8093158
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 144 -
Rwork0.282 2319 -
all-2463 -
obs--99.8 %
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)
14.4491-2.418-1.48242.20711.14563.3268-0.0301-0.56120.32850.2620.3534-0.43890.1840.5967-0.32340.1267-0.0032-0.05240.2636-0.02640.398728.172-74.382194.962
21.484-0.4884-0.13284.176-0.90771.2037-0.05140.14930.1819-0.55610.13670.02010.0486-0.0071-0.08520.1057-0.0629-0.04610.17180.03550.265516.03-59.694175.933
31.9047-0.4809-0.17151.35570.19171.1942-0.03830.00690.00420.04470.01110.0588-0.00060.01350.02710.0068-0.01370.00710.0392-0.00820.2375-1.046-70.514210.119
44.77811.2282-0.00466.41111.79496.1775-0.19290.17810.108-0.4350.4564-0.4404-0.50940.7461-0.26340.1995-0.0920.09660.2513-0.00310.339327.199-32.858178.238
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 83
2X-RAY DIFFRACTION2A84 - 301
3X-RAY DIFFRACTION3B0 - 999
4X-RAY DIFFRACTION4C0 - 999

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