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- PDB-6sg4: Structure of CDK2/cyclin A M246Q, S247EN -

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Basic information

Entry
Database: PDB / ID: 6sg4
TitleStructure of CDK2/cyclin A M246Q, S247EN
Components
  • Cyclin-A2
  • Cyclin-dependent kinase 2
KeywordsCELL CYCLE / cyclin-dependent kinases / cancer / cyclin a / cdk2 / skp2
Function / homology
Function and homology information


Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine ...Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / 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 DNA replication / regulation of anaphase-promoting complex-dependent catabolic process / 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 / cellular response to nitric oxide / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / 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 / 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 / cellular response to estradiol stimulus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / potassium ion transport / 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 / Meiotic recombination / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / cellular senescence / positive regulation of fibroblast proliferation / 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 / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / DNA replication / transcription regulator complex / chromosome, telomeric region / Ub-specific processing proteases / endosome / chromatin remodeling / protein domain specific binding / cell division / protein phosphorylation / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription
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
Cyclin-A2 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsSalamina, M. / Basle, A. / Massa, B. / Noble, M.E.M. / Endicott, J.A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust063551 United Kingdom
Medical Research Council (MRC, United Kingdom)G0901526 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N009738/1 United Kingdom
Cancer Research UKC2115/A21421 United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Discriminative SKP2 Interactions with CDK-Cyclin Complexes Support a Cyclin A-Specific Role in p27KIP1 Degradation.
Authors: Salamina, M. / Montefiore, B.C. / Liu, M. / Wood, D.J. / Heath, R. / Ault, J.R. / Wang, L.Z. / Korolchuk, S. / Basle, A. / Pastok, M.W. / Reeks, J. / Tatum, N.J. / Sobott, F. / Arold, S.T. / ...Authors: Salamina, M. / Montefiore, B.C. / Liu, M. / Wood, D.J. / Heath, R. / Ault, J.R. / Wang, L.Z. / Korolchuk, S. / Basle, A. / Pastok, M.W. / Reeks, J. / Tatum, N.J. / Sobott, F. / Arold, S.T. / Pagano, M. / Noble, M.E.M. / Endicott, J.A.
History
DepositionAug 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)130,9274
Polymers130,9274
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-35 kcal/mol
Surface area45630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.309, 137.853, 109.774
Angle α, β, γ (deg.)90.00, 99.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein Cyclin-A2 / Cyclin-A / Cyclin A


Mass: 31108.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Production host: Escherichia coli (E. coli) / References: UniProt: P20248
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 200 mM K/Na Tartrate, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.43→85.1 Å / Num. obs: 44281 / % possible obs: 99.6 % / Redundancy: 1.9 % / CC1/2: 0.997 / Net I/σ(I): 12
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4672 / CC1/2: 0.528 / % possible all: 98.7

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Processing

Software
NameClassification
DIALSdata reduction
xia2data reduction
pointlessdata scaling
Aimlessdata scaling
PHASERphasing
REFMACrefinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JST

1jst


Resolution: 2.43→85.1 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 22.541 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.506 / ESU R Free: 0.278 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25075 2129 4.8 %RANDOM
Rwork0.20092 ---
obs0.20326 42143 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.606 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å2-0 Å20.54 Å2
2---0.47 Å20 Å2
3----1.41 Å2
Refinement stepCycle: 1 / Resolution: 2.43→85.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8383 0 0 97 8480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138602
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178159
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.64311690
X-RAY DIFFRACTIONr_angle_other_deg1.1121.5718953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5551033
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86222.567413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.144151502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8731541
X-RAY DIFFRACTIONr_chiral_restr0.0580.21106
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029342
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021741
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5722.0414150
X-RAY DIFFRACTIONr_mcbond_other0.5722.0414149
X-RAY DIFFRACTIONr_mcangle_it1.0333.0575176
X-RAY DIFFRACTIONr_mcangle_other1.0333.0585177
X-RAY DIFFRACTIONr_scbond_it0.4532.0884452
X-RAY DIFFRACTIONr_scbond_other0.4532.0884450
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8163.1146513
X-RAY DIFFRACTIONr_long_range_B_refined2.21523.3689157
X-RAY DIFFRACTIONr_long_range_B_other2.20623.3429146
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 166 -
Rwork0.29 3130 -
obs--99.1 %
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)
12.15720.2141-0.21483.0924-0.24812.51960.0285-0.0976-0.1156-0.0936-0.05360.16560.0409-0.26380.02510.0173-0.029-0.00050.0829-0.01010.1043-9.2221-14.5453-45.4811
21.7241-0.50310.85372.2614-0.33093.33550.083-0.07420.0856-0.0054-0.0228-0.0431-0.2226-0.0787-0.06020.0535-0.00710.04250.0413-0.01390.1756-3.926318.4481-39.9891
31.9236-0.1595-0.44933.34451.07063.2492-0.04310.0451-0.23820.20060.1296-0.33130.04020.5799-0.08650.08870.0869-0.02060.30870.02510.25629.0369-15.7136-93.1092
41.89970.1520.18552.3844-0.66663.80.1868-0.11380.14020.3894-0.0883-0.0473-0.52740.0154-0.09850.3696-0.01490.05780.19750.04810.20424.472816.8234-100.7845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 294
2X-RAY DIFFRACTION2B175 - 432
3X-RAY DIFFRACTION3C29 - 295
4X-RAY DIFFRACTION4D175 - 432

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