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- PDB-8ern: Cyclin-free CDK2 in complex with Cpd21 -

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Basic information

Entry
Database: PDB / ID: 8ern
TitleCyclin-free CDK2 in complex with Cpd21
ComponentsCyclin-dependent kinase 2
KeywordsTRANSFERASE / kinase / SBDD
Function / homology
Function and homology information


cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation ...cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cellular response to nitric oxide / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cajal body / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / : / meiotic cell cycle / positive regulation of DNA replication / male germ cell nucleus / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / DNA replication / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / chromosome, telomeric region / endosome / chromatin remodeling / protein domain specific binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / DNA-templated transcription / centrosome / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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
Chem-WQK / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMurray, J.M. / Oh, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cyclin-free CDK2 in complex with Cpd21
Authors: Murray, J.M. / Oh, A.
History
DepositionOct 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6553
Polymers34,1241
Non-polymers5322
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.681, 72.655, 71.702
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cyclin-dependent kinase 2 / Cell division protein kinase 2 / p33 protein kinase


Mass: 34123.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24941, cyclin-dependent kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-WQK / N,3-dimethyl-4-({7-[(2S)-2-methylpyrrolidine-1-carbonyl]quinazolin-2-yl}amino)benzene-1-sulfonamide


Mass: 439.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25N5O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15-20% PEG 4K, 50mM Hepes pH 7.5 50mM Ammonium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.64→51.04 Å / Num. obs: 29490 / % possible obs: 83.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 25.09 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.7
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 6.3 % / Rmerge(I) obs: 2.275 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1744 / CC1/2: 0.38 / Rpim(I) all: 0.977 / Rrim(I) all: 2.479 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B39

1b39


Resolution: 1.64→36.33 Å / SU ML: 0.3317 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.3549
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2503 1460 4.96 %
Rwork0.2075 27955 -
obs0.2098 29415 83.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.52 Å2
Refinement stepCycle: LAST / Resolution: 1.64→36.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 37 107 2463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752435
X-RAY DIFFRACTIONf_angle_d0.94733310
X-RAY DIFFRACTIONf_chiral_restr0.053369
X-RAY DIFFRACTIONf_plane_restr0.0076438
X-RAY DIFFRACTIONf_dihedral_angle_d15.1579923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.690.4091580.37983256X-RAY DIFFRACTION98.44
1.7-1.760.32811260.33492780X-RAY DIFFRACTION83.51
1.76-1.840.34551900.29393303X-RAY DIFFRACTION99.94
1.84-1.930.3211760.26881559X-RAY DIFFRACTION49.74
1.96-2.040.28231140.21652336X-RAY DIFFRACTION98.71
2.09-2.220.27321340.20982711X-RAY DIFFRACTION99.37
2.22-2.440.26111560.20662941X-RAY DIFFRACTION88.06
2.44-2.80.27231520.21952704X-RAY DIFFRACTION80.75
2.8-3.520.24561780.19583149X-RAY DIFFRACTION93.04
3.53-36.330.20541760.17273216X-RAY DIFFRACTION90.84
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)
10.624353994921-0.1626928719910.06686476630060.3133926819540.222587310660.638730644391-0.149228818058-0.109167773993-0.0373132647174-0.220799609197-0.123450192014-0.8658619676140.1446904423050.321510798359-0.001363316086760.33215599840.0440713820099-0.004679258033280.3900975109920.05067511292720.52635035867718.8287450018-18.725751084911.3382506094
20.436222803449-0.1382336965810.2764264101180.9218918664831.041677958152.16892147686-0.0185634227731-0.1195195361650.0508722868346-0.02199325016810.336815059922-0.786923273551-0.4550696187131.028821631470.06599338064530.321351250936-0.0127572469851-0.012621968710.578048842166-0.05318855294810.55299253987225.7125949124-8.0860182025516.370626925
31.3596828856-0.374822313331-0.3559445714272.822302937870.3575624883931.51943084633-0.06666256305690.043740526321-0.2521413777890.02235396166940.0825229787651-0.01651804434580.06716629519380.158103012584-0.0006747781546650.1893866380810.00913280758864-0.01187891384040.1973824803770.01937381646440.17004739583210.3639207932-3.7349818355416.0322576382
41.22941528729-0.3301026770070.7694017635352.887081538054.734281914989.20290378398-0.01778451167550.5673585559330.571775296046-0.914308033210.531778973846-0.934044172692-1.17950976821.744639794571.234486912290.591635932913-0.0937736238132-0.008904787573620.5288296140060.1207119489910.65283494397819.94152253940.28696498126911.5336183911
50.7336222881750.4316296749290.1725324991910.68259319855-0.3323355268291.207441745730.1148551875180.388079510537-0.522917876673-0.3196511182890.00435504575755-0.8348734618880.5477487431150.9073098647180.07744772028250.3636572494360.06043840680470.02840151186460.338813943475-0.02891695670740.36410693034118.7996923228.459435421645.40284453717
60.899320285906-0.0174232273093-0.4616967966741.36466177873-0.672818792580.590110135650.03029439117550.1535627921750.187813539205-0.1891506646210.0581162111466-0.02674237929680.00572607340479-0.01791857096080.0001055057169850.212790248158-0.0009740408088330.01113433106380.2110227208260.0183461175730.1957412365310.091054787318.13458190584.99171147879
70.108056251771-0.122516959311-0.07740350625350.1424754343770.0806071771950.1213930431660.1510094130430.1994231924440.186713585087-0.36900611394-0.1448340017310.244567216318-0.182467803039-0.3432281801580.0004272424765110.2572475265670.0309159767931-0.01798107627950.281463010257-0.0001600677704050.285542554515-3.1694326232915.789179919212.851253613
81.1383378888-0.73843159477-0.1090964767551.00732027869-0.7106449287521.40076961668-0.0472951142601-0.06064852912370.0253835706857-0.009728276726620.066067652360.245524323748-0.0465247427976-0.0250838398238-0.0001616115735160.204420497406-0.011284978980.03819654299860.201451524889-0.01187652390920.1816869647222.350454826089.7591694473120.0274647498
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: B

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 28 )0 - 281 - 29
22chain 'A' and (resid 29 through 57 )29 - 5730 - 49
33chain 'A' and (resid 58 through 140 )58 - 14050 - 132
44chain 'A' and (resid 141 through 157 )141 - 157133 - 149
55chain 'A' and (resid 158 through 181 )158 - 181150 - 173
66chain 'A' and (resid 182 through 247 )182 - 247174 - 239
77chain 'A' and (resid 248 through 266 )248 - 266240 - 258
88chain 'A' and (resid 267 through 296 )267 - 296259 - 288

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