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- PDB-4ii5: Structure of PCDK2/CYCLINA bound to ADP and 1 MAGNESIUM ION -

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Basic information

Entry
Database: PDB / ID: 4ii5
TitleStructure of PCDK2/CYCLINA bound to ADP and 1 MAGNESIUM ION
Components
  • Cyclin-A2
  • Cyclin-dependent kinase 2
KeywordsTransferase/Cell Cycle / ADP AND MAGNESIUM BINDING / T160 PHOSPHORYLATION / Transferase-Cell Cycle complex
Function / homology
Function and homology information


G0 and Early G1 / Telomere Extension By Telomerase / Regulation of APC/C activators between G1/S and early anaphase / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / G2 Phase / p53-Dependent G1 DNA Damage Response / Cyclin A:Cdk2-associated events at S phase entry / Cyclin A/B1/B2 associated events during G2/M transition / DNA Damage/Telomere Stress Induced Senescence / Regulation of TP53 Degradation ...G0 and Early G1 / Telomere Extension By Telomerase / Regulation of APC/C activators between G1/S and early anaphase / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / G2 Phase / p53-Dependent G1 DNA Damage Response / Cyclin A:Cdk2-associated events at S phase entry / Cyclin A/B1/B2 associated events during G2/M transition / DNA Damage/Telomere Stress Induced Senescence / Regulation of TP53 Degradation / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / CDK-mediated phosphorylation and removal of Cdc6 / Orc1 removal from chromatin / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / Regulation of TP53 Activity through Phosphorylation / mitotic cell cycle phase transition / Ub-specific processing proteases / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / cochlea development / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cellular response to platelet-derived growth factor stimulus / 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 / regulation of DNA replication / 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 / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / Cajal body / cyclin-dependent kinase / animal organ regeneration / 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 / 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 / response to organic substance / cellular response to estradiol stimulus / G1/S transition of mitotic cell cycle / 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 / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / DNA replication
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-like ...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-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
ADENOSINE-5'-DIPHOSPHATE / Cyclin-dependent kinase 2 / Cyclin-A2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJacobsen, D.M. / Bao, Z.-Q. / O'Brien, P.J. / Brooks III, C.L. / Young, M.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Price to be paid for two-metal catalysis: Magnesium ions that accelerate chemistry unavoidably limit product release from a PROTEIN KINASE
Authors: Jacobsen, D.M. / Bao, Z.-Q. / O'Brien, P.J. / Brooks III, C.L. / Young, M.A.
History
DepositionDec 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: 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
B: Cyclin-A2
C: Cyclin-dependent kinase 2
D: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,76516
Polymers127,1254
Non-polymers1,64012
Water9,314517
1
A: Cyclin-dependent kinase 2
B: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2907
Polymers63,5632
Non-polymers7285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-30 kcal/mol
Surface area23340 Å2
MethodPISA
2
C: Cyclin-dependent kinase 2
D: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4759
Polymers63,5632
Non-polymers9127
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-30 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.140, 164.140, 73.450
Angle α, β, γ (deg.)90.00, 107.04, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:296 )
211chain C and (resseq 1:296 )
112chain B and (resseq 175:430 )
212chain D and (resseq 175:430 )

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 34056.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein Cyclin-A2 / Cyclin-A


Mass: 29506.062 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 165-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ccna, Ccna2, Cyca / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P51943

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Non-polymers , 4 types, 529 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O

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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: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% W/V POLYACRYLIC ACID SODIUM SALT 5100, 20MM MGCL2, 100MM HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 22, 2010
RadiationMonochromator: DIAMOND LAUE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.15→29.56 Å / Num. obs: 83087 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 3.6 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.133 / Net I/σ(I): 6.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→29.56 Å / SU ML: 0.32 / Isotropic thermal model: isotropic plus TLS / Cross valid method: R-free set maintained throughout / σ(F): 0 / σ(I): 1.5 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 2007 2.42 %PHENIX selected about 2000 reflections distributed roughly equally among the shells
Rwork0.1997 ---
all0.2004 ---
obs0.2004 83087 95.3 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.641 Å2 / ksol: 0.392 e/Å3
Displacement parametersBiso mean: 45.2 Å2
Baniso -1Baniso -2Baniso -3
1-9.618 Å20 Å25.181 Å2
2---7.6602 Å2-0 Å2
3----1.9577 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8896 0 104 517 9517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019230
X-RAY DIFFRACTIONf_angle_d1.16812540
X-RAY DIFFRACTIONf_dihedral_angle_d16.0363440
X-RAY DIFFRACTIONf_chiral_restr0.0861415
X-RAY DIFFRACTIONf_plane_restr0.0061565
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2382X-RAY DIFFRACTIONPOSITIONAL
12C2382X-RAY DIFFRACTIONPOSITIONAL0.078
21B2068X-RAY DIFFRACTIONPOSITIONAL
22D2068X-RAY DIFFRACTIONPOSITIONAL0.082
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.15-2.20380.35011290.33835219521986
2.2038-2.26330.31391440.31685281528188
2.2633-2.32990.33021170.28795433543390
2.3299-2.40510.2541390.25765544554492
2.4051-2.4910.30381460.2555663566394
2.491-2.59070.29281390.23335860586096
2.5907-2.70850.24911550.22455902590297
2.7085-2.85120.23391540.19655994599498
2.8512-3.02960.24371420.19135991599199
3.0296-3.26330.22771440.18225995599599
3.2633-3.59120.22581480.18096036603699
3.5912-4.10960.2111540.17086048604899
4.1096-5.17320.15571520.1556045604599
5.1732-29.560.19331440.19296069606998
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)
10.9530.41440.8780.3850.75511.58390.61660.0552-0.29070.77570.01220.0108-0.24090.122-0.22570.6333-0.07530.29420.2619-0.01080.713715.3563-76.8196-29.7356
20.0405-0.22540.03320.4381-0.25250.43490.2429-0.0533-0.0211-0.1157-0.1597-0.66770.2014-0.0091-0.10780.3128-0.04610.05840.17550.00550.348611.4645-76.9965-26.3784
30.41320.07740.34250.74530.01530.8131-0.0667-0.0285-0.0657-0.05190.0134-0.16340.3018-0.12060.05340.3229-0.01950.07860.1510.00170.18810.5207-67.8802-36.0153
40.56450.5945-0.14211.6062-0.21240.3346-0.01340.03270.1957-0.0377-0.0025-0.04720.0698-0.0749-0.02160.22130.00030.05150.12560.01070.1773-2.1711-48.9364-41.6772
50.63-0.2385-0.08690.56040.12490.1836-0.08180.4444-0.0198-0.1197-0.1809-0.1634-0.081-0.43390.04610.3866-0.08010.06580.30150.02790.1698-19.4335-66.4169-28.3889
60.11280.09710.28630.1553-0.10890.3527-0.0593-0.0047-0.00070.34880.09350.1531-0.0371-0.1330.02030.443-0.01880.09230.14570.00710.149-10.1148-70.7831-5.511
70.1983-0.05230.19880.4015-0.00190.20030.07950.0498-0.11850.21010.0861-0.1010.02690.0702-0.0490.4651-0.03680.01830.159-0.03030.20140.5307-68.928-8.0772
80.45880.20290.12480.14310.3340.6379-0.1293-0.0823-0.05190.11920.16930.1195-0.1465-0.4615-0.27440.41080.01930.1280.33730.05390.2107-28.1208-60.7024-13.756
9-0.0549-0.08040.0580.05630.22240.4529-0.9713-0.24361.02250.63220.2863-0.4138-0.614-0.348-0.09250.61670.21630.45940.3061-0.0328-0.2133-23.7693-54.5117-0.7846
100.26050.1011-0.0360.0283-0.00030.03990.08010.08290.08070.2284-0.19610.44110.65-0.21130.04471.0575-0.0281-0.26070.1330.03770.4963-6.6583-14.2941.8859
110.226-0.2888-0.03040.1148-0.02970.24820.1012-0.0720.1379-0.6298-0.01040.41860.143-0.0265-0.10320.5597-0.0351-0.06020.19590.01190.361-5.2845-14.06226.8317
120.30840.1714-0.03080.70690.04260.53660.05910.05220.0405-0.47330.01450.0005-0.26440.03620.00340.4430.00580.0140.1705-0.00630.16269.2983-22.98484.9545
130.13040.14990.32651.00690.2720.4554-0.0040.0096-0.1731-0.37910.0580.06440.00270.07140.16080.5164-0.00380.08980.158-0.0290.218114.9617-41.87141.8563
140.378-0.5164-0.13381.38140.94741.1341-0.07720.3502-0.0169-0.4635-0.0788-0.1849-0.27050.04140.00370.2019-0.02270.08470.1902-0.05290.17921.6515-23.964322.3664
150.3067-0.0765-0.45770.67360.32360.1968-0.0852-0.05180.00790.32130.12610.12860.01740.1351-0.01030.29010.00330.04320.15410.00450.17621.1129-19.908936.1809
160.2347-0.2945-0.14750.56430.2060.123-0.12430.12690.07380.05050.02690.07350.0832-0.02810.07320.2727-0.02020.02970.1690.01060.2802-6.2695-21.987928.1527
170.5780.3377-0.20150.6308-0.55150.4874-0.2215-0.2297-0.1190.14930.1455-0.10790.05910.02220.04920.25670.08380.00080.2049-0.00760.195820.8746-29.527739.4148
180.5113-0.1934-0.18740.4103-0.37410.2872-0.2781-0.3193-0.50980.21960.3160.0957-0.0356-0.04530.03440.52040.11620.10240.27510.06360.230110.6897-35.780147.8875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:17)
2X-RAY DIFFRACTION2chain 'A' and (resseq 18:45)
3X-RAY DIFFRACTION3chain 'A' and (resseq 46:158)
4X-RAY DIFFRACTION4chain 'A' and (resseq 159:296)
5X-RAY DIFFRACTION5chain 'B' and (resseq 175:192)
6X-RAY DIFFRACTION6chain 'B' and (resseq 193:268)
7X-RAY DIFFRACTION7chain 'B' and (resseq 269:310)
8X-RAY DIFFRACTION8chain 'B' and (resseq 311:399)
9X-RAY DIFFRACTION9chain 'B' and (resseq 400:430)
10X-RAY DIFFRACTION10chain 'C' and (resseq 1:17)
11X-RAY DIFFRACTION11chain 'C' and (resseq 18:45)
12X-RAY DIFFRACTION12chain 'C' and (resseq 46:158)
13X-RAY DIFFRACTION13chain 'C' and (resseq 159:296)
14X-RAY DIFFRACTION14chain 'D' and (resseq 175:192)
15X-RAY DIFFRACTION15chain 'D' and (resseq 193:268)
16X-RAY DIFFRACTION16chain 'D' and (resseq 269:310)
17X-RAY DIFFRACTION17chain 'D' and (resseq 311:399)
18X-RAY DIFFRACTION18chain 'D' and (resseq 400:431)

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