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- PDB-8h4r: The Crystal Structure of CDK3 and CyclinE1 Complex with Dinacicli... -

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Basic information

Entry
Database: PDB / ID: 8h4r
TitleThe Crystal Structure of CDK3 and CyclinE1 Complex with Dinaciclib from Biortus
Components
  • G1/S-specific cyclin-E1
  • Glutathione S-transferase class-mu 26 kDa isozyme,Cyclin-dependent kinase 3
KeywordsCELL CYCLE / complex
Function / homology
Function and homology information


positive regulation of mesenchymal stem cell proliferation / G0 to G1 transition / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / G1/S-Specific Transcription / cyclin E1-CDK2 complex / negative regulation of Notch signaling pathway / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / p53-Dependent G1 DNA Damage Response ...positive regulation of mesenchymal stem cell proliferation / G0 to G1 transition / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / G1/S-Specific Transcription / cyclin E1-CDK2 complex / negative regulation of Notch signaling pathway / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / p53-Dependent G1 DNA Damage Response / PTK6 Regulates Cell Cycle / Association of TriC/CCT with target proteins during biosynthesis / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / glutathione transferase / G0 and Early G1 / glutathione transferase activity / DNA replication initiation / cyclin-dependent protein kinase holoenzyme complex / positive regulation of G1/S transition of mitotic cell cycle / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cyclin E associated events during G1/S transition / regulation of G2/M transition of mitotic cell cycle / telomere maintenance / cyclin binding / : / G1/S transition of mitotic cell cycle / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Wnt signaling pathway / Cyclin D associated events in G1 / regulation of protein localization / kinase activity / regulation of gene expression / cell population proliferation / cell division / protein phosphorylation / protein serine kinase activity / centrosome / DNA damage response / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Glutathione S-transferase, C-terminal domain / Cyclin, N-terminal / Cyclin, N-terminal domain / Glutathione S-transferase, N-terminal domain ...Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Glutathione S-transferase, C-terminal domain / Cyclin, N-terminal / Cyclin, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-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
Chem-1QK / Glutathione S-transferase class-mu 26 kDa isozyme / G1/S-specific cyclin-E1 / Cyclin-dependent kinase 3
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGui, W. / Wang, F. / Cheng, W. / Gao, J. / Huang, Y. / Ouyang, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of CDK3 and CyclinE1 Complex with Dinaciclib from Biortus
Authors: Gui, W. / Wang, F. / Cheng, W. / Gao, J. / Huang, Y. / Ouyang, Z.
History
DepositionOct 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 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: Glutathione S-transferase class-mu 26 kDa isozyme,Cyclin-dependent kinase 3
B: G1/S-specific cyclin-E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,84812
Polymers97,4952
Non-polymers1,35310
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-95 kcal/mol
Surface area23230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.027, 155.027, 76.788
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Glutathione S-transferase class-mu 26 kDa isozyme,Cyclin-dependent kinase 3 / GST 26 / Sj26 antigen / SjGST / Cell division protein kinase 3


Mass: 61776.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata), (gene. exp.) Homo sapiens (human)
Gene: CDK3, CDKN3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P08515, UniProt: Q00526, glutathione transferase, cyclin-dependent kinase
#2: Protein G1/S-specific cyclin-E1


Mass: 35718.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNE1, CCNE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24864

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Non-polymers , 5 types, 283 molecules

#3: Chemical ChemComp-1QK / 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium / DINACICLIB / Dinaciclib


Mass: 397.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6M MgSO4, 0.1M MES pH 6.60

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.75→44.75 Å / Num. obs: 27244 / % possible obs: 99.1 % / Redundancy: 4 % / CC1/2: 0.976 / Net I/σ(I): 7.3
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3956 / CC1/2: 0.577 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→42.371 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.161 / SU B: 9.316 / SU ML: 0.179 / Average fsc free: 0.9638 / Average fsc work: 0.9798 / Cross valid method: FREE R-VALUE / ESU R: 0.409 / ESU R Free: 0.274
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2234 1385 5.085 %
Rwork0.1614 25852 -
all0.164 --
obs-27237 98.846 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.299 Å2
Baniso -1Baniso -2Baniso -3
1-0.571 Å20.285 Å20 Å2
2--0.571 Å2-0 Å2
3----1.851 Å2
Refinement stepCycle: LAST / Resolution: 2.75→42.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4577 0 83 273 4933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124778
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164460
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.6456480
X-RAY DIFFRACTIONr_angle_other_deg0.3611.56110394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7785564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.838527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84910851
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.6410211
X-RAY DIFFRACTIONr_chiral_restr0.050.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025229
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02937
X-RAY DIFFRACTIONr_nbd_refined0.1940.21049
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24339
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22354
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22492
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2163
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0410.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.211
X-RAY DIFFRACTIONr_nbd_other0.1560.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.27
X-RAY DIFFRACTIONr_mcbond_it5.2733.4952250
X-RAY DIFFRACTIONr_mcbond_other5.2733.4952250
X-RAY DIFFRACTIONr_mcangle_it7.9395.2292810
X-RAY DIFFRACTIONr_mcangle_other7.9395.2312811
X-RAY DIFFRACTIONr_scbond_it6.8654.1052528
X-RAY DIFFRACTIONr_scbond_other6.8644.1062529
X-RAY DIFFRACTIONr_scangle_it10.185.9063668
X-RAY DIFFRACTIONr_scangle_other10.1795.9073669
X-RAY DIFFRACTIONr_lrange_it14.22767.44420132
X-RAY DIFFRACTIONr_lrange_other14.2467.41919984
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
2.75-2.8210.279850.26919120.2720170.9390.95299.00840.269
2.821-2.8980.2871060.22918370.23219610.950.96699.08210.229
2.898-2.9820.31090.22217950.22619250.9380.96798.90910.222
2.982-3.0730.298850.20117350.20518470.9360.97398.53820.201
3.073-3.1730.218980.18516670.18717880.970.97898.71360.185
3.173-3.2840.2791020.1816350.18617440.9520.9899.59860.18
3.284-3.4070.198890.16415850.16616880.9750.98499.17060.164
3.407-3.5450.2880.15615250.15916180.9740.98699.6910.156
3.545-3.7020.216680.14514930.14815640.9710.98799.80820.145
3.702-3.8810.243610.14414180.14814830.9660.98799.73030.144
3.881-4.0890.177710.12613430.12814240.9810.9999.29780.126
4.089-4.3340.19900.1212490.12413500.9780.99199.18520.12
4.334-4.630.13480.10812010.10912610.9910.99399.04840.108
4.63-4.9960.186610.11911210.12211910.980.99299.24430.119
4.996-5.4660.187520.14310160.14510930.9810.98897.71270.143
5.466-6.0980.266460.1659190.1699830.9620.98498.16890.165
6.098-7.0170.223420.1768380.1798950.9750.98198.3240.176
7.017-8.5360.207450.156800.1537480.9760.98696.92510.15
8.536-11.8340.217170.1215680.1235970.9670.99197.990.121
11.834-42.3710.257220.223150.2223690.9590.97291.32790.22

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