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- PDB-2cch: The crystal structure of CDK2 cyclin A in complex with a substrat... -

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Basic information

Entry
Database: PDB / ID: 2cch
TitleThe crystal structure of CDK2 cyclin A in complex with a substrate peptide derived from CDC modified with a gamma-linked ATP analogue
Components
  • (CELL DIVISION ...) x 2
  • CYCLIN A2
KeywordsCELL CYCLE / COMPLEX(TRANSFERASE-CELL DIVISION) / ATP-BINDING / CDK2 / CELL DIVISION / CYCLIN / MITOSIS / NUCLEAR PROTEIN / PEPTIDE SPECIFICITY / PHOSPHORYLATION / POLYMORPHISM / PROTEIN KINASE / RECRUITMENT / SERINE-THREONINE-PROTEIN KINASE / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE
Function / homology
Function and homology information


positive regulation of chromosome segregation / cellular response to vasopressin / CDC6 association with the ORC:origin complex / 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 / traversing start control point of mitotic cell cycle / mitotic cell cycle phase transition / DNA replication checkpoint signaling ...positive regulation of chromosome segregation / cellular response to vasopressin / CDC6 association with the ORC:origin complex / 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 / traversing start control point of mitotic cell cycle / mitotic cell cycle phase transition / DNA replication checkpoint signaling / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / Transcription of E2F targets under negative control by DREAM complex / mitotic DNA replication checkpoint signaling / male pronucleus / female pronucleus / cellular response to angiotensin / cellular response to cocaine / regulation of mitotic metaphase/anaphase transition / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of DNA biosynthetic process / cellular response to insulin-like growth factor stimulus / regulation of cyclin-dependent protein serine/threonine kinase activity / intercellular bridge / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cochlea development / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / negative regulation of DNA replication / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / G1/S-Specific Transcription / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / positive regulation of cytokinesis / regulation of anaphase-promoting complex-dependent catabolic process / regulation of DNA replication / cellular response to platelet-derived growth factor stimulus / 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 / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / DNA replication initiation / cellular response to nitric oxide / Activation of the pre-replicative complex / spindle midzone / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / animal organ regeneration / 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 / Cajal body / Cyclin A/B1/B2 associated events during G2/M transition / cyclin-dependent protein kinase holoenzyme complex / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of G2/M transition of mitotic cell cycle / regulation of mitotic cell cycle / post-translational protein modification / cyclin binding / positive regulation of DNA replication / male germ cell nucleus / meiotic cell cycle / cellular response to estradiol stimulus / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / mitotic spindle / Meiotic recombination / CDK-mediated phosphorylation and removal of Cdc6 / kinase binding / SCF(Skp2)-mediated degradation of p27/p21 / spindle pole / Transcriptional regulation of granulopoiesis / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / 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)
Similarity search - Function
Cell division protein Cdc6/18 / : / Cdc6/ORC-like, ATPase lid domain / CDC6, C terminal / Cdc6, C-terminal / CDC6, C terminal winged helix domain / Orc1-like, AAA ATPase domain / AAA ATPase domain / : / Cyclin-A, N-terminal APC/C binding region ...Cell division protein Cdc6/18 / : / Cdc6/ORC-like, ATPase lid domain / CDC6, C terminal / Cdc6, C-terminal / CDC6, C terminal winged helix domain / Orc1-like, AAA ATPase domain / AAA ATPase 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, 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 / : / Winged helix DNA-binding domain 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. / Winged helix-like DNA-binding domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Cyclin-A2 / Cyclin-dependent kinase 2 / Cell division control protein 6 homolog
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCheng, K.Y. / Noble, M.E.M. / Skamnaki, V. / Brown, N.R. / Lowe, E.D. / Kontogiannis, L. / Shen, K. / Cole, P.A. / Siligardi, G. / Johnson, L.N.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Role of the Phospho-Cdk2/Cyclin a Recruitment Site in Substrate Recognition
Authors: Cheng, K.Y. / Noble, M.E.M. / Skamnaki, V. / Brown, N.R. / Lowe, E.D. / Kontogiannis, L. / Shen, K. / Cole, P.A. / Siligardi, G. / Johnson, L.N.
History
DepositionJan 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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: CELL DIVISION CONTROL PROTEIN 6 HOMOLOG
F: CELL DIVISION CONTROL PROTEIN 6 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,23611
Polymers130,9426
Non-polymers1,2955
Water18,8261045
1
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
E: CELL DIVISION CONTROL PROTEIN 6 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2587
Polymers65,4713
Non-polymers7874
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2
F: CELL DIVISION CONTROL PROTEIN 6 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9784
Polymers65,4713
Non-polymers5071
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.535, 114.483, 181.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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CELL DIVISION ... , 2 types, 4 molecules ACEF

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


Mass: 34143.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATED ON THR160 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#3: Protein/peptide CELL DIVISION CONTROL PROTEIN 6 HOMOLOG / CDC6-BIS / CDC6-RELATED PROTEIN / P62 / CDC6 / HSCDC6 / HSCDC18


Mass: 1459.696 Da / Num. of mol.: 2
Fragment: PEPTIDE DERIVED FROM SUBSTRATE/RECRUITMENT REGION OF CDC6 RESIDUE 89-100
Source method: obtained synthetically
Details: GAMMA PHOSPHATE OF ATP IS COVALENTLY ATTACHED BY A LINKER TO THE AMINO ANALOGUE OF THE OH ACCEPTOR AMINO ACID LOCATED IN THE CDC6 SUBSTRATE PEPTIDE
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q99741

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Protein , 1 types, 2 molecules BD

#2: Protein CYCLIN A2 / CYCLIN-A


Mass: 29867.512 Da / Num. of mol.: 2 / Fragment: CYCLIN FOLD FRAGMENT RESIDUES 175-432
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: P20248

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Non-polymers , 4 types, 1050 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1045 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCHAINS B AND D ARE A TRUNCATED FRAGMENT OF CYCLIN A2 CONSISTING OF RESIDUES 175-432 CHAINS E AND F ...CHAINS B AND D ARE A TRUNCATED FRAGMENT OF CYCLIN A2 CONSISTING OF RESIDUES 175-432 CHAINS E AND F ARE PEPTIDES REPRESENTING A FRAGMENT FROM RESIDUES 89-100 OF CDC6

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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: 2.9 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 13% PEG MONOMETHYLETHER 5000, 0.2 M AMMONIUM SULPHATE, 0.1 M CITRATE/ACETATE BUFFER PH 5.6 AT 4 C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.96865
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96865 Å / Relative weight: 1
ReflectionResolution: 1.7→96 Å / Num. obs: 167702 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.1
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.8 / % possible all: 91.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QMZ

1qmz


Resolution: 1.7→96.67 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.295 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 8410 5 %RANDOM
Rwork0.148 ---
obs0.15 159215 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---1.23 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.7→96.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9148 0 79 1045 10272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0229738
X-RAY DIFFRACTIONr_bond_other_d0.0010.028867
X-RAY DIFFRACTIONr_angle_refined_deg1.591.99313282
X-RAY DIFFRACTIONr_angle_other_deg0.894320708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70151180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07823.937414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.909151692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7641548
X-RAY DIFFRACTIONr_chiral_restr0.1490.21491
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210594
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021934
X-RAY DIFFRACTIONr_nbd_refined0.2330.22272
X-RAY DIFFRACTIONr_nbd_other0.1940.29091
X-RAY DIFFRACTIONr_nbtor_refined0.180.24886
X-RAY DIFFRACTIONr_nbtor_other0.0860.25208
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2860
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3560.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3450.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3640.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6741.57571
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98329521
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.95734587
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8954.53761
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.25 550
Rwork0.184 10178

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