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- PDB-1h26: CDK2/CyclinA in complex with an 11-residue recruitment peptide fr... -

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Basic information

Entry
Database: PDB / ID: 1h26
TitleCDK2/CyclinA in complex with an 11-residue recruitment peptide from p53
Components
  • CELL DIVISION PROTEIN KINASE 2
  • CELLULAR TUMOR ANTIGEN P53
  • CYCLIN A2
KeywordsCELL CYCLE / PROTEIN KINASE / CYCLIN / CDK2 / RECRUITMENT / PEPTIDE SPECIFICITY
Function / homology
Function and homology information


: / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / male pronucleus / Regulation of TP53 Expression ...: / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / male pronucleus / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / female pronucleus / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / oligodendrocyte apoptotic process / negative regulation of miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / mRNA transcription / bone marrow development / positive regulation of programmed necrotic cell death / circadian behavior / T cell proliferation involved in immune response / cellular response to cocaine / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / glucose catabolic process to lactate via pyruvate / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / response to glucagon / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / positive regulation of DNA biosynthetic process / cyclin-dependent protein serine/threonine kinase regulator activity / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / thymocyte apoptotic process / B cell lineage commitment / TP53 Regulates Transcription of Caspase Activators and Caspases / cellular response to insulin-like growth factor stimulus / cardiac septum morphogenesis / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / negative regulation of mitophagy / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / negative regulation of DNA replication / G2 Phase / Y chromosome / entrainment of circadian clock by photoperiod / 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 / PTK6 Regulates Cell Cycle / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / regulation of anaphase-promoting complex-dependent catabolic process / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / TFIID-class transcription factor complex binding / Regulation of APC/C activators between G1/S and early anaphase / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / regulation of DNA replication / telomere maintenance in response to DNA damage / microtubule organizing center / centrosome duplication / rRNA transcription / negative regulation of reactive oxygen species metabolic process / Transcriptional Regulation by VENTX / cellular response to UV-C / replicative senescence / G0 and Early G1 / general transcription initiation factor binding
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-like / Cyclin, C-terminal domain / Cyclin_C ...Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / Cyclin A; domain 1 / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / Cyclin, N-terminal / Cyclin, N-terminal domain / p53-like transcription factor, DNA-binding / 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
Cellular tumor antigen p53 / Cyclin-A2 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsTews, I. / Cheng, K.Y. / Lowe, E.D. / Noble, M.E.M. / Brown, N.R. / Gul, S. / Gamblin, S. / Johnson, L.N.
Citation
Journal: Biochemistry / Year: 2002
Title: Specificity Determinants of Recruitment Peptides Bound to Phospho-Cdk2/Cyclin A
Authors: Lowe, E.D. / Tews, I. / Cheng, K.Y. / Brown, N.R. / Gul, S. / Noble, M.E.M. / Gamblin, S. / Johnson, L.N.
#1: Journal: Nat.Cell Biol. / Year: 1999
Title: The Structural Basis for Specificity of Substrate and Recruitment Peptides for Cyclin-Dependant Kinases
Authors: Brown, N.R. / Noble, M.E.M. / Endicott, J.A. / Johnson, L.N.
History
DepositionJul 31, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 1.4Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2
E: CELLULAR TUMOR ANTIGEN P53


Theoretical massNumber of molelcules
Total (without water)129,8105
Polymers129,8105
Non-polymers00
Water3,477193
1
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
E: CELLULAR TUMOR ANTIGEN P53


Theoretical massNumber of molelcules
Total (without water)65,5893
Polymers65,5893
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2


Theoretical massNumber of molelcules
Total (without water)64,2212
Polymers64,2212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.667, 134.035, 147.936
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.02073, -0.48795, 0.87263), (0.51071, 0.75552, 0.41033), (-0.8595, 0.43716, 0.26486)6.3783, -58.74466, 48.2543
2given(0.02673, -0.50623, 0.86198), (0.48829, 0.75903, 0.43063), (-0.87227, 0.40939, 0.26748)9.386, -60.03935, 51.67831
DetailsBIOMOLECULE 1 IS A TRIMERIC COMPLEX OF CHAINS A, B AND E. BIOMOLECULE 2 IS A DIMERIC COMPLEX OF CHAINS C AND D

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Components

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


Mass: 34467.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATED ON THR160 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834
References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein CYCLIN A2 / CYCLIN A


Mass: 29753.410 Da / Num. of mol.: 2 / Fragment: CYCLIN FOLD, RESIDUES 175-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET21D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P20248
#3: Protein/peptide CELLULAR TUMOR ANTIGEN P53 / P53 RECRUITMENT PEPTIDE 11MER


Mass: 1367.682 Da / Num. of mol.: 1 / Fragment: RESIDUES 376-386 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P04637
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCDK2: CONTROL OF THE CELL CYCLE DURING S PHASE AND G2. BELONGS TO THE SER/THR FAMILY OF PROTEIN ...CDK2: CONTROL OF THE CELL CYCLE DURING S PHASE AND G2. BELONGS TO THE SER/THR FAMILY OF PROTEIN KINASES. CYCLIN A2: CONTROL OF THE CELL CYCLE. INTERACTS WITH THE CDK2 AND CDC2 PROTEIN KINASES. P53: TRANSCRIPTION ACTIVATOR INVOLVED IN CELL CYCLE REGULATION AND DNA REPLICATION.
Has protein modificationY
Sequence detailsCHAINS B AND D ARE A TRUNCATED FRAGMENT OF CYCLIN A2 CONSISTING OF RESIDUES 175-432

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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: 3.1 Å3/Da / Density % sol: 59.8 %
Crystal growpH: 7
Details: 0.8M KCL, 1.2M (NH4)2SO4, 40MM HEPES PH 7.0. PROTEIN CONCENTRATION = 10MG/ML
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMHEPES1droppH7.4
3150 mM1dropNaCl
43.4 mMEDTA1drop
50.01 %azide1drop
60.01 %monothiglycerol1drop
70.8 M1reservoirKCl
81.2 Mammonium sulfate1reservoir
9100 mMHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.24→29.88 Å / Num. obs: 63733 / % possible obs: 96.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.1
Reflection shellResolution: 2.24→2.36 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.3 / % possible all: 75.5
Reflection
*PLUS
Highest resolution: 2.24 Å / Lowest resolution: 29.88 Å / Num. measured all: 223072 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 75.5 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QMZ

1qmz


Resolution: 2.24→29.88 Å / SU B: 15.477 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R Free: 0.231
RfactorNum. reflection% reflectionSelection details
Rfree0.268 3458 5.1 %RANDOM
Rwork0.216 ---
obs0.219 64823 96.49 %-
Displacement parametersBiso mean: 44.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.24→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8788 0 0 193 8981
Refinement
*PLUS
Highest resolution: 2.24 Å / Lowest resolution: 29.88 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7
LS refinement shell
*PLUS
Highest resolution: 2.244 Å / Lowest resolution: 2.302 Å / Rfactor Rfree: 0.381 / Rfactor Rwork: 0.253 / Num. reflection Rwork: 168 / Total num. of bins used: 20

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