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- PDB-9et3: CDK2-cyclin A in complex with FragLite 10 -

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Basic information

Entry
Database: PDB / ID: 9et3
TitleCDK2-cyclin A in complex with FragLite 10
Components
  • Cyclin-A2
  • Cyclin-dependent kinase 2
KeywordsCELL CYCLE / cyclin-dependent kinase / FragLite / CDK2 / cyclin A / Fragment
Function / homology
Function and homology information


cell cycle G1/S phase transition / cyclin-dependent protein serine/threonine kinase regulator activity / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / cyclin-dependent protein kinase activity / G2 Phase / Y chromosome ...cell cycle G1/S phase transition / cyclin-dependent protein serine/threonine kinase regulator activity / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / cyclin-dependent protein kinase activity / G2 Phase / 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) / microtubule organizing center / centriole replication / regulation of DNA replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / 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 / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / condensed chromosome / regulation of G2/M transition of mitotic cell cycle / mitotic G1 DNA damage checkpoint signaling / cellular response to nitric oxide / post-translational protein modification / cyclin binding / regulation of mitotic cell cycle / male germ cell nucleus / positive regulation of DNA replication / meiotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / Orc1 removal from chromatin / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / peptidyl-serine phosphorylation / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / chromosome, telomeric region / DNA replication / endosome / protein phosphorylation / chromatin remodeling / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / DNA-templated transcription / positive regulation of cell population proliferation / centrosome / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal ...Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like 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
6-bromo-1,3-dihydro-2H-indol-2-one / Cyclin-dependent kinase 2 / Cyclin-A2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsHope, I. / Martin, M.P. / Waring, M.J. / Noble, M.E.M. / Endicott, J.A. / Tatum, N.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N009738/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/V029142/1 United Kingdom
Cancer Research UKC2115/A21421 United Kingdom
CitationJournal: To Be Published
Title: Crystallographic fragment screening of CDK2-cyclin A: FragLites map sites of protein-protein interaction
Authors: Hope, I. / Martin, M.P. / Waring, M.J. / Noble, M.E.M. / Endicott, J.A. / Tatum, N.J.
History
DepositionMar 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Cyclin-A2
A: Cyclin-dependent kinase 2
B: Cyclin-A2
C: Cyclin-dependent kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,31318
Polymers130,3444
Non-polymers2,96914
Water5,368298
1
D: Cyclin-A2
C: Cyclin-dependent kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4458
Polymers65,1722
Non-polymers1,2726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-20 kcal/mol
Surface area22160 Å2
MethodPISA
2
A: Cyclin-dependent kinase 2
B: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,86910
Polymers65,1722
Non-polymers1,6968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-16 kcal/mol
Surface area23400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.121, 133.849, 148.042
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cyclin-A2 / Cyclin-A


Mass: 30817.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CCNA2 / Plasmid: PET21d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30274
#2: Protein Cyclin-dependent kinase 2 / Cell division protein kinase 2 / p33 protein kinase


Mass: 34354.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Plasmid: PGEX6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24941, cyclin-dependent kinase
#3: Chemical
ChemComp-1P8 / 6-bromo-1,3-dihydro-2H-indol-2-one


Mass: 212.043 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: C8H6BrNO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein at 10 mg/ml. 0.6 to 0.8 M KCl, 0.9 to 1.2 M (NH4)2SO4, and 100 mM HEPES pH 7.0
PH range: 7-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91839 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91839 Å / Relative weight: 1
ReflectionResolution: 2.34→148.04 Å / Num. obs: 59478 / % possible obs: 94.4 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Net I/σ(I): 16.8
Reflection shellResolution: 2.34→2.4 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.624 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4870 / CC1/2: 0.658 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→99.483 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.17 / Average fsc free: 0.9573 / Average fsc work: 0.9706 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.217 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2214 3102 5.222 %
Rwork0.1829 56301 -
all0.185 --
obs-59403 94.398 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 58.129 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å20 Å2
2--0.164 Å20 Å2
3---0.896 Å2
Refinement stepCycle: LAST / Resolution: 2.34→99.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8711 0 154 298 9163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0129134
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.84212417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40151081
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.756544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.943101574
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.58310390
X-RAY DIFFRACTIONr_chiral_restr0.1180.21383
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026876
X-RAY DIFFRACTIONr_nbd_refined0.2220.24319
X-RAY DIFFRACTIONr_nbtor_refined0.3180.26110
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2432
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2560.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2130.212
X-RAY DIFFRACTIONr_mcbond_it5.1655.4744336
X-RAY DIFFRACTIONr_mcangle_it7.5389.8215413
X-RAY DIFFRACTIONr_scbond_it7.176.14798
X-RAY DIFFRACTIONr_scangle_it10.29810.9687004
X-RAY DIFFRACTIONr_lrange_it13.68760.54713940
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.34-2.4010.32470.27343700.27446170.9370.9481000.266
2.401-2.4670.3052320.26142570.26344890.9320.9531000.251
2.467-2.5380.2992020.24641350.24843370.9460.9591000.231
2.538-2.6160.3062210.24539870.24842080.9360.9611000.226
2.616-2.7020.3021320.25524260.25841160.9440.96162.14770.231
2.702-2.7970.2392030.2137680.21139710.9640.9721000.188
2.797-2.9020.2812100.22436440.22738540.9440.9681000.198
2.902-3.020.2582080.21534770.21736850.9550.971000.192
3.02-3.1550.2711750.20933780.21235530.9460.9721000.188
3.155-3.3080.2081780.18732420.18834200.9720.9781000.171
3.308-3.4870.2171120.18221460.18432430.9710.97969.62690.168
3.487-3.6980.2171440.16723400.1730950.9710.98480.25850.157
3.698-3.9530.1891410.15823950.15928900.980.98587.75090.149
3.953-4.2690.1911280.14825850.1527130.980.9871000.144
4.269-4.6760.1731310.13223720.13525030.9830.9891000.132
4.676-5.2270.1771160.1421560.14222720.980.9881000.142
5.227-6.0320.2331000.16719310.1720310.9730.9841000.167
6.032-7.3810.197980.17616480.17717460.9760.9821000.18
7.381-10.410.157810.15612860.15613670.9880.9861000.172
10.41-99.4830.295430.2377580.248180.9380.96297.92180.269

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