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- PDB-4yc3: CDK1/CyclinB1/CKS2 Apo -

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Basic information

Entry
Database: PDB / ID: 4yc3
TitleCDK1/CyclinB1/CKS2 Apo
Components
  • Cyclin-dependent kinase 1
  • Cyclin-dependent kinases regulatory subunit 2
  • G2/mitotic-specific cyclin-B1
KeywordsCELL CYCLE / CDK1 / Cyclin B1 / CKS2
Function / homology
Function and homology information


regulation of Schwann cell differentiation / 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 / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / G2/M DNA replication checkpoint ...regulation of Schwann cell differentiation / 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 / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / ventricular cardiac muscle cell development / 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 / Phosphorylation of Emi1 / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / patched binding / Nuclear Pore Complex (NPC) Disassembly / Transcriptional regulation by RUNX2 / Phosphorylation of the APC/C / outer kinetochore / meiosis I / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Initiation of Nuclear Envelope (NE) Reformation / protein localization to kinetochore / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / cyclin-dependent protein serine/threonine kinase activator activity / Condensation of Prometaphase Chromosomes / response to copper ion / chromosome condensation / centrosome cycle / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / SCF ubiquitin ligase complex / mitotic metaphase chromosome alignment / G1/S-Specific Transcription / cyclin-dependent protein kinase activity / MAPK3 (ERK1) activation / response to amine / ubiquitin-like protein ligase binding / mitotic G2 DNA damage checkpoint signaling / Regulation of APC/C activators between G1/S and early anaphase / regulation of embryonic development / cellular response to organic cyclic compound / response to axon injury / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / Nuclear events stimulated by ALK signaling in cancer / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / response to cadmium ion / Cyclin A/B1/B2 associated events during G2/M transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle cell proliferation / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / epithelial cell differentiation / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / Hsp70 protein binding / APC/C:Cdc20 mediated degradation of Cyclin B / ERK1 and ERK2 cascade / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / Condensation of Prophase Chromosomes / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / mitotic spindle organization / positive regulation of DNA replication / ubiquitin binding / response to activity / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / peptidyl-threonine phosphorylation / MAPK6/MAPK4 signaling / PKR-mediated signaling / spindle microtubule / regulation of circadian rhythm / response to toxic substance / mitotic spindle / spindle pole / positive regulation of protein import into nucleus / microtubule cytoskeleton organization / cellular response to hydrogen peroxide / positive regulation of protein localization to nucleus / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition
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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
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 / Resolution: 2.7 Å
AuthorsBrown, N.R. / Korolchuk, S. / Martin, M.P. / Stanley, W. / Moukhametzianov, R. / Noble, M.E.M. / Endicott, J.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0901526 United Kingdom
Cancer Research UKC240/A15751 United Kingdom
Astex PharmaceuticalsNICR-Alliance United Kingdom
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 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)76,4515
Polymers76,2143
Non-polymers2362
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-39 kcal/mol
Surface area29990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.200, 70.150, 156.200
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
Details: GST-fusion protein cleaved by 3C protease / 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 / Fragment: UNP residues 165-433
Source method: isolated from a genetically manipulated source
Details: N-terminal His tag removed by thrombin cleavage / 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
Source method: isolated from a genetically manipulated source
Details: N-terminal GST tag removed by 3C protease cleavage / Source: (gene. exp.) Homo sapiens (human) / Gene: CKS2 / Plasmid: GST-3C / Production host: Escherichia coli (E. coli) / References: UniProt: P33552
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.7
Details: 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: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.7→52.19 Å / Num. all: 21241 / Num. obs: 21241 / % possible obs: 98.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 6.6
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.5 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.7→52.19 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.879 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 1100 5.2 %RANDOM
Rwork0.2113 20095 --
obs0.2138 21195 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.86 Å2 / Biso mean: 40.9313 Å2 / Biso min: 3.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2--0.59 Å20 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 2.7→52.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5159 0 16 212 5387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0195329
X-RAY DIFFRACTIONr_bond_other_d00.025219
X-RAY DIFFRACTIONr_angle_refined_deg2.2211.9757207
X-RAY DIFFRACTIONr_angle_other_deg3.672312018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2475634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.62423.734241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.29815989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5291533
X-RAY DIFFRACTIONr_chiral_restr0.1520.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215861
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021214
X-RAY DIFFRACTIONr_mcbond_it0.8721.0092539
X-RAY DIFFRACTIONr_mcbond_other0.8721.0092538
X-RAY DIFFRACTIONr_mcangle_it1.5961.5073172
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 65 -
Rwork0.352 1275 -
all-1340 -
obs--85.57 %
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)
13.76912.2021-2.44554.3349-2.08175.72450.3816-1.00640.31561.1259-0.56270.2471-0.7422-0.13790.18110.3712-0.0176-0.02330.5108-0.06280.518517.42410.883186.46
25.4526-0.53111.57182.71-0.16942.41710.2994-0.219-0.33320.1556-0.12040.02820.2990.1803-0.17890.2059-0.0035-0.08630.0470.01420.314633.224-10.999179.579
312.240811.85382.559111.83142.40160.99940.0873-0.01231.1210.5438-0.00981.33070.1656-0.3256-0.07750.7831-0.05840.08740.444-0.00190.584913.9-31.771175.322
41.7643-0.3082-0.84491.76330.11183.07880.02120.25920.0054-0.04340.0079-0.07350.1762-0.0759-0.02920.0198-0.0037-0.03320.05580.03780.323522.82318.612154.877
55.6336-0.93640.0475.3091-1.73546.11710.1826-0.44180.14250.6251-0.3705-0.387-0.07750.75670.18780.1337-0.0848-0.07610.49810.18840.39659.887-5.624189.88
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 84
2X-RAY DIFFRACTION2A85 - 286
3X-RAY DIFFRACTION3A287 - 297
4X-RAY DIFFRACTION4B166 - 430
5X-RAY DIFFRACTION5C4 - 75

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