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- PDB-7xqk: The Crystal Structure of CDK3 and CyclinE1 Complex from Biortus. -

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Basic information

Entry
Database: PDB / ID: 7xqk
TitleThe Crystal Structure of CDK3 and CyclinE1 Complex 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 / cyclin E1-CDK2 complex / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / p53-Dependent G1 DNA Damage Response / G1/S-Specific Transcription / PTK6 Regulates Cell Cycle ...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 / cyclin E1-CDK2 complex / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / p53-Dependent G1 DNA Damage Response / G1/S-Specific Transcription / PTK6 Regulates Cell Cycle / Association of TriC/CCT with target proteins during biosynthesis / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / microtubule organizing center / glutathione transferase / G0 and Early G1 / glutathione transferase activity / negative regulation of Notch signaling pathway / DNA replication initiation / 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 / cyclin-dependent protein kinase holoenzyme complex / regulation of G2/M transition of mitotic cell cycle / glutathione metabolic process / 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 / kinase activity / regulation of protein localization / regulation of gene expression / cell population proliferation / protein phosphorylation / cell division / protein serine kinase activity / DNA damage response / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
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 ...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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Cyclin-like superfamily / 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
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: 2.25 Å
AuthorsGui, W. / Wang, F. / Cheng, W. / Gao, J. / Huang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Structural basis of CDK3 activation by cyclin E1 and inhibition by dinaciclib.
Authors: Gui, W. / Hang, Y. / Cheng, W. / Gao, M. / Wu, J. / Ouyang, Z.
History
DepositionMay 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary
Category: pdbx_contact_author / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_contact_author.email / _pdbx_entry_details.has_protein_modification
Revision 1.3Nov 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)99,02317
Polymers97,4952
Non-polymers1,52815
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-146 kcal/mol
Surface area24020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.154, 154.154, 76.675
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 , 4 types, 443 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


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


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6M MgSO4, 0.1M MES pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18078 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18078 Å / Relative weight: 1
ReflectionResolution: 2.25→44.5 Å / Num. obs: 49467 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.139 / Net I/σ(I): 15.9
Reflection shellResolution: 2.25→2.32 Å / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4563 / CC1/2: 0.797

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EOJ

4eoj


Resolution: 2.25→44.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.962 / SU ML: 0.099 / Cross valid method: FREE R-VALUE / ESU R: 0.162 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2024 2457 4.969 %
Rwork0.1599 46990 -
all0.162 --
obs-49447 99.97 %
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: 38.105 Å2
Baniso -1Baniso -2Baniso -3
1-0.355 Å20.178 Å20 Å2
2--0.355 Å2-0 Å2
3----1.153 Å2
Refinement stepCycle: LAST / Resolution: 2.25→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4580 0 85 428 5093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134825
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154636
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.6366551
X-RAY DIFFRACTIONr_angle_other_deg1.3071.57510693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7622.065247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05615866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3681530
X-RAY DIFFRACTIONr_chiral_restr0.0780.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021091
X-RAY DIFFRACTIONr_nbd_refined0.2080.21037
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.24416
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22319
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22125
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2304
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.219
X-RAY DIFFRACTIONr_nbd_other0.2360.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.218
X-RAY DIFFRACTIONr_mcbond_it3.3023.7172265
X-RAY DIFFRACTIONr_mcbond_other3.3023.7152264
X-RAY DIFFRACTIONr_mcangle_it5.0645.5552833
X-RAY DIFFRACTIONr_mcangle_other5.0635.5582834
X-RAY DIFFRACTIONr_scbond_it4.154.2182560
X-RAY DIFFRACTIONr_scbond_other4.1494.2192561
X-RAY DIFFRACTIONr_scangle_it6.4116.1283711
X-RAY DIFFRACTIONr_scangle_other6.416.1293712
X-RAY DIFFRACTIONr_lrange_it9.48743.5695564
X-RAY DIFFRACTIONr_lrange_other9.47743.2935477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.3080.2271750.2163485X-RAY DIFFRACTION99.8908
2.308-2.3720.2442050.1993336X-RAY DIFFRACTION100
2.372-2.440.2371590.1853276X-RAY DIFFRACTION100
2.44-2.5150.2191480.1713198X-RAY DIFFRACTION100
2.515-2.5980.2241440.173091X-RAY DIFFRACTION100
2.598-2.6890.191550.1563015X-RAY DIFFRACTION100
2.689-2.7910.2261580.162860X-RAY DIFFRACTION100
2.791-2.9040.2351490.1632775X-RAY DIFFRACTION100
2.904-3.0340.2121320.1632671X-RAY DIFFRACTION99.9643
3.034-3.1820.1991460.1652533X-RAY DIFFRACTION100
3.182-3.3540.221370.1642418X-RAY DIFFRACTION100
3.354-3.5570.1841260.1552283X-RAY DIFFRACTION99.9585
3.557-3.8020.1941230.1522160X-RAY DIFFRACTION100
3.802-4.1070.1591050.1372018X-RAY DIFFRACTION100
4.107-4.4980.17800.1231863X-RAY DIFFRACTION100
4.498-5.0280.172900.1311692X-RAY DIFFRACTION100
5.028-5.8050.216980.1721469X-RAY DIFFRACTION100
5.805-7.1060.222580.1871277X-RAY DIFFRACTION100
7.106-10.0350.178440.144999X-RAY DIFFRACTION100
10.035-44.50.233250.201571X-RAY DIFFRACTION98.5124

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