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- PDB-1w98: The structural basis of CDK2 activation by cyclin E -

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Basic information

Entry
Database: PDB / ID: 1w98
TitleThe structural basis of CDK2 activation by cyclin E
Components
  • CELL DIVISION PROTEIN KINASE 2
  • G1/S-SPECIFIC CYCLIN E1
KeywordsTRANSFERASE / CELL CYCLE
Function / homology
Function and homology information


positive regulation of mesenchymal stem cell proliferation / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / 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 / G2 Phase ...positive regulation of mesenchymal stem cell proliferation / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / 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 / G2 Phase / Y chromosome / cyclin-dependent protein kinase activity / 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 / G1/S-Specific Transcription / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / Association of TriC/CCT with target proteins during biosynthesis / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / microtubule organizing center / centrosome duplication / G0 and Early G1 / Telomere Extension By Telomerase / DNA replication initiation / Activation of the pre-replicative 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 / Cajal body / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / 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 / telomere maintenance / post-translational protein modification / cyclin binding / regulation of mitotic cell cycle / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / G1/S transition of mitotic cell cycle / peptidyl-serine phosphorylation / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / G2/M transition of mitotic cell cycle / Wnt signaling pathway / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / kinase activity / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / regulation of protein localization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / transcription regulator complex / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / chromosome, telomeric region / DNA replication / protein phosphorylation / endosome / chromatin remodeling / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / positive regulation of cell population proliferation / DNA-templated transcription / centrosome / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion 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-like / Cyclin, C-terminal domain / Cyclin_C / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain ...Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
G1/S-specific cyclin-E1 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLowe, E.D. / Honda, R. / Dubinina, E. / Skamnaki, V. / Cook, A. / Johnson, L.N.
CitationJournal: Embo J. / Year: 2005
Title: The Structure of Cyclin E1/Cdk2: Implications for Cdk2 Activation and Cdk2-Independent Roles
Authors: Honda, R. / Lowe, E.D. / Dubinina, E. / Skamnaki, V. / Cook, A. / Brown, N. / Johnson, L.N.
History
DepositionOct 7, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELL DIVISION PROTEIN KINASE 2
B: G1/S-SPECIFIC CYCLIN E1


Theoretical massNumber of molelcules
Total (without water)66,9402
Polymers66,9402
Non-polymers00
Water9,854547
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-19.6 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.620, 99.620, 149.987
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CELL DIVISION PROTEIN KINASE 2 / CYCLIN DEPENDENT KINASE 2 / P33 PROTEIN KINASE


Mass: 34030.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PHOSPHOTHREONINE AT POSITION 160 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24941, EC: 2.7.1.37
#2: Protein G1/S-SPECIFIC CYCLIN E1 / CYCLIN E


Mass: 32909.371 Da / Num. of mol.: 1
Fragment: FRAGMENT DERIVED FROM ELASTASE CLEAVAGE, RESIDUES 96-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P24864
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAN ADDITIONAL SER RESIDUE FROM THE EXPRESSION CONSTRUCT IS PRESENT AT POSITION 0 THIS FRAGMENT ...AN ADDITIONAL SER RESIDUE FROM THE EXPRESSION CONSTRUCT IS PRESENT AT POSITION 0 THIS FRAGMENT CONTAINS ONLY RESIDUES 81-363

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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: 2.8 Å3/Da / Density % sol: 56 %
Description: MR SEARCH MODEL MODIFIED TO CONTAIN ONLY THE N- TERMINAL CYCLIN BOX DOMAIN OF CYCLIN A
Crystal growpH: 7.5
Details: PCDK2/CYCLIN E (6-8 MG/ML), 1 MM AMPPNP, 10-15% PEG3350, 0.2 M SODIUM CITRATE PH7.5, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0091
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0091 Å / Relative weight: 1
ReflectionResolution: 2.13→34.28 Å / Num. obs: 39329 / % possible obs: 94.2 % / Observed criterion σ(I): 1.5 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 2.13→2.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9 / % possible all: 53.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JST

1jst


Resolution: 2.15→83.05 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 11 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1984 5 %RANDOM
Rwork0.181 ---
obs0.185 37310 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.15→83.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4617 0 0 547 5164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224735
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9556429
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5855566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55623.886211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.05115838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4571525
X-RAY DIFFRACTIONr_chiral_restr0.1220.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023526
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.22512
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23179
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2485
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8741.52943
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41124622
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.23232076
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2584.51807
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.339 80
Rwork0.216 1221
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)
10.68840.69150.15592.11840.24711.66870.14940.02540.00710.1109-0.1012-0.18280.13280.3431-0.0482-0.12160.0091-0.00780.060.0005-0.020941.596114.0014-4.6329
22.15991.27771.79820.79631.46395.44750.02160.1963-0.2821-0.22570.2108-0.10160.04180.7312-0.2324-0.10830.00850.03470.0369-0.01880.040336.872818.4936-19.9836
34.83563.32982.17445.8134-0.32351.91940.16050.172-0.18230.21810.04940.04040.07010.1385-0.2099-0.0820.02210.0241-0.02660.0051-0.007321.92718.7975-15.5924
41.67410.3178-0.45211.63520.19930.92770.03850.17270.196-0.1140.0252-0.0104-0.13760.0344-0.0637-0.0466-0.0180.0112-0.01110.0436-0.064521.779529.458-19.7737
51.0444-0.42020.26061.22220.00881.36540.018-0.0245-0.0131-0.01250.03520.11360.0664-0.0807-0.0532-0.0573-0.0348-0.0059-0.00090.02-0.03136.857818.5636-13.701
618.0814-10.74078.11219.1165-1.21038.39810.66760.2190.4086-1.3147-0.2452-0.23520.2210.3144-0.42240-0.05420.1027-0.05510.0161-0.093228.60656.5788-32.4256
71.9268-0.00831.03510.93560.19342.46090.39210.153-0.27340.15680.0717-0.14250.54350.2436-0.46380.07290.1229-0.1669-0.0715-0.0848-0.002935.8152-10.6859-11.9726
87.9995-0.79516.59766.37822.85947.40290.09730.46791.1882-0.178-0.102-0.0228-0.18330.42880.0047-0.08270.05980.07930.071-0.0208-0.042435.77951.5776-19.1421
92.5410.88022.5150.7731.36974.69190.63730.5949-0.39460.1850.1855-0.07190.84370.3939-0.82280.08870.1625-0.1893-0.0352-0.1058-0.06523.4223-13.293-29.136
106.4955-15.0552-8.928348.502343.406850.1833-0.31460.2246-0.2796-0.2289-1.36064.1171-0.9269-1.94281.6752-0.01050.00070.110.14240.22220.029627.506223.4914-41.3511
1110.643310.169811.268918.14617.786417.7761-0.62421.02862.2491-1.4192-0.59522.3239-2.2409-0.36751.21940.10460.0989-0.15810.12780.17230.218411.8243.1492-30.5756
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 57
2X-RAY DIFFRACTION1A67 - 82
3X-RAY DIFFRACTION2A58 - 66
4X-RAY DIFFRACTION3A122 - 127
5X-RAY DIFFRACTION3A146 - 164
6X-RAY DIFFRACTION4A83 - 121
7X-RAY DIFFRACTION4A128 - 145
8X-RAY DIFFRACTION4A245 - 288
9X-RAY DIFFRACTION4A190 - 202
10X-RAY DIFFRACTION5A165 - 189
11X-RAY DIFFRACTION5A203 - 244
12X-RAY DIFFRACTION6B88 - 113
13X-RAY DIFFRACTION7B114 - 223
14X-RAY DIFFRACTION8B224 - 230
15X-RAY DIFFRACTION9B231 - 243
16X-RAY DIFFRACTION9B257 - 357
17X-RAY DIFFRACTION10A289 - 297
18X-RAY DIFFRACTION11B244 - 256

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