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- PDB-1h28: CDK2/CyclinA in complex with an 11-residue recruitment peptide fr... -

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Basic information

Entry
Database: PDB / ID: 1h28
TitleCDK2/CyclinA in complex with an 11-residue recruitment peptide from p107
Components
  • CELL DIVISION PROTEIN KINASE 2
  • CYCLIN A2
  • RETINOBLASTOMA-LIKE PROTEIN 1
KeywordsCELL CYCLE/TRANSFERASE SUBSTRATE / CELL CYCLE / PROTEIN KINASE / CYCLIN / CDK2 / RECRUITMENT / PEPTIDE SPECIFICITY / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / CELL DIVISION / MITOSIS / PHOSPHORYLATION / CELL CYCLE-TRANSFERASE SUBSTRATE / CELL CYCLE-TRANSFERASE SUBSTRATE COMPLEX
Function / homology
Function and homology information


regulation of lipid kinase activity / : / 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 / male pronucleus / female pronucleus / Transcription of E2F targets under negative control by DREAM complex ...regulation of lipid kinase activity / : / 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 / male pronucleus / female pronucleus / Transcription of E2F targets under negative control by DREAM complex / cellular response to cocaine / response to glucagon / positive regulation of DNA biosynthetic process / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / negative regulation of G1/S transition of mitotic cell cycle / 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 / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / microtubule organizing center / regulation of DNA replication / telomere maintenance in response to DNA damage / centrosome duplication / negative regulation of cellular senescence / G0 and Early G1 / cochlea development / Telomere Extension By Telomerase / animal organ regeneration / Activation of the pre-replicative complex / 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 / cellular response to platelet-derived growth factor stimulus / mitotic G1 DNA damage checkpoint signaling / cellular response to nitric oxide / post-translational protein modification / cyclin binding / regulation of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / promoter-specific chromatin binding / cellular response to estradiol stimulus / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / G1/S transition of mitotic cell cycle / peptidyl-serine phosphorylation / DNA Damage/Telomere Stress Induced Senescence / potassium ion transport / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / G2/M transition of mitotic cell cycle / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / Cyclin D associated events in G1 / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / chromatin organization / Processing of DNA double-strand break ends / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / transcription regulator complex / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / cell differentiation / chromosome, telomeric region / DNA replication / protein phosphorylation / endosome
Similarity search - Function
Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) ...Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) / Retinoblastoma-associated protein A domain / Rb C-terminal domain / 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; 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
Cyclin-A2 / Cyclin-dependent kinase 2 / Retinoblastoma-like protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / 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

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: RETINOBLASTOMA-LIKE PROTEIN 1
F: RETINOBLASTOMA-LIKE PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)130,8316
Polymers130,8316
Non-polymers00
Water66737
1
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
E: RETINOBLASTOMA-LIKE PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)65,4163
Polymers65,4163
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2
F: RETINOBLASTOMA-LIKE PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)65,4163
Polymers65,4163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)149.503, 162.514, 71.375
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99999, -0.00049, 0.0036), (-0.00048, -1, -0.00121), (0.0036, 0.00121, -0.99999)-0.03242, 0.00121, -0.99999
2given(0.99999, 0.00063, 0.00345), (0.00062, -0.99999, 0.00414), (0.00345, -0.00414, -0.99999)-0.05151, 154.78839, 35.96083

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Components

#1: Protein CELL DIVISION PROTEIN KINASE 2 / CYCLIN-DEPENDENT KINASE 2 / P33 PROTEIN KINASE / CDK2


Mass: 34467.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P24941
#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 RETINOBLASTOMA-LIKE PROTEIN 1 / 107 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN / PRB1 / P107 / P107 RECRUITMENT PEPTIDE 11MER


Mass: 1194.365 Da / Num. of mol.: 2 / Fragment: RB PEPTIDE, RESIDUES 653-663 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P28749
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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. P107: INVOLVED IN G1 ARREST.
Has protein modificationY
Sequence detailsMOLECULE IS A TRUNCATED FRAGMENT OF CYCLIN A3 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: 3.6 Å3/Da / Density % sol: 65.7 %
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: ID14-4 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→28.99 Å / Num. obs: 41507 / % possible obs: 95.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 2.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 1.2 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 92651
Reflection shell
*PLUS
% possible obs: 97.8 %

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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: 2.8→29.62 Å / SU B: 13.287 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 1.245 / ESU R Free: 0.45
RfactorNum. reflection% reflectionSelection details
Rfree0.323 2095 5 %RANDOM
Rwork0.243 ---
obs0.247 39408 95.1 %-
Displacement parametersBiso mean: 30.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.06 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9088 0 0 37 9125
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 29.6 Å / Rfactor Rfree: 0.327 / Rfactor Rwork: 0.266
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.84
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.872 Å / Rfactor Rfree: 0.398 / Num. reflection Rfree: 141 / Rfactor Rwork: 0.302 / Num. reflection Rwork: 2950 / Total num. of bins used: 20

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