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- PDB-1gy3: pCDK2/cyclin A in complex with MgADP, nitrate and peptide substrate -

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Basic information

Entry
Database: PDB / ID: 1gy3
TitlepCDK2/cyclin A in complex with MgADP, nitrate and peptide substrate
Components
  • CELL DIVISION PROTEIN KINASE 2
  • CYCLIN A2
  • SUBSTRATE PEPTIDE
KeywordsTRANSFERASE/TRANSFERASE SUBSTRATE / TRANSFERASE-TRANSFERASE SUBSTRATE COMPLEX / CELL CYCLE REGULATORY PROTEIN KINASE / THR160-PHOSPHO-CYCLIN DEPENDENT PROTEIN KINASE 2 IN ASSOCIATION WITH CYCLIN A / TRANSFERASE- TRANSFERASE SUBSTRATE COMPLEX
Function / homologyTranscription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / Protein kinase-like domain superfamily / Senescence-Associated Secretory Phenotype (SASP) / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of APC/C activators between G1/S and early anaphase / Activation of ATR in response to replication stress / Cyclin-like / Protein kinase, ATP binding site / Cdc20:Phospho-APC/C mediated degradation of Cyclin A ...Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / Protein kinase-like domain superfamily / Senescence-Associated Secretory Phenotype (SASP) / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of APC/C activators between G1/S and early anaphase / Activation of ATR in response to replication stress / Cyclin-like / Protein kinase, ATP binding site / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / G0 and Early G1 / Ub-specific processing proteases / Cyclin-A, N-terminal / Protein kinase domain profile. / Cyclin-like superfamily / Cyclin / Cyclins signature. / Serine/Threonine protein kinases active-site signature. / Protein kinases ATP-binding region signature. / N-terminal region of cyclin_N / Cyclin, C-terminal domain / DNA Damage/Telomere Stress Induced Senescence / Processing of DNA double-strand break ends / Protein kinase domain / Cyclin, C-terminal domain / Factors involved in megakaryocyte development and platelet production / Meiotic recombination / PTK6 Regulates Cell Cycle / Cyclin A:Cdk2-associated events at S phase entry / p53-Dependent G1 DNA Damage Response / Protein kinase domain / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin E associated events during G1/S transition / Cyclin, N-terminal / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Serine/threonine-protein kinase, active site / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / CDK-mediated phosphorylation and removal of Cdc6 / Activation of the pre-replicative complex / Orc1 removal from chromatin / G2 Phase / Regulation of TP53 Degradation / Regulation of TP53 Activity through Phosphorylation / Cyclin, N-terminal domain / cellular response to luteinizing hormone stimulus / cellular response to cocaine / cell cycle G1/S phase transition / male pronucleus / female pronucleus / cellular response to insulin-like growth factor stimulus / cellular response to leptin stimulus / cochlea development / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to platelet-derived growth factor stimulus / regulation of DNA replication / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of mitotic nuclear division / cyclin E1-CDK2 complex / cyclin E2-CDK2 complex / cyclin A1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-dependent DNA replication initiation / Y chromosome / cyclin-dependent protein kinase activity / X chromosome / histone phosphorylation / centrosome duplication / centriole replication / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Cajal body / condensed chromosome / cellular response to nitric oxide / cyclin binding / mitotic G1 DNA damage checkpoint / positive regulation of cell cycle / regulation of gene silencing / potassium ion transport / meiotic cell cycle / cellular response to estradiol stimulus / chromosome, telomeric region / animal organ regeneration / G1/S transition of mitotic cell cycle / positive regulation of fibroblast proliferation / anaphase-promoting complex-dependent catabolic process / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Ras protein signal transduction / cellular response to hypoxia / regulation of G2/M transition of mitotic cell cycle / mitotic cell cycle / transcription factor complex / G2/M transition of mitotic cell cycle / regulation of signal transduction by p53 class mediator / DNA replication / endosome / peptidyl-serine phosphorylation / protein deubiquitination / centrosome
Function and homology information
Specimen sourceHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.7 Å resolution
AuthorsCook, A. / Lowe, E.D. / Chrysina, E.D. / Skamnaki, V.T. / Oikonomakos, N.G. / Johnson, L.N.
Citation
Journal: Biochemistry / Year: 2002
Title: Structural Studies on Phospho-Cdk2/Cyclin a Bound to Nitrate, a Transition State Analogue: Implications for the Protein Kinase Mechanism
Authors: Cook, A. / Lowe, E.D. / Chrysina, E.D. / Skamnaki, V.T. / Oikonomakos, N.G. / Johnson, L.N.
#1: Journal: Nat.Cell Biol. / Year: 1999
Title: The Structural Basis for Specificity of Substrate and Recruitment Peptides Fo Cyclin-Dependent Kinases
Authors: Brown, N.R. / Noble, M.E.M. / Endicott, J.A. / Johnson, L.N.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 19, 2002 / Release: Apr 29, 2002
RevisionDateData content typeGroupProviderType
1.0Apr 29, 2002Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelAtomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance

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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: SUBSTRATE PEPTIDE
F: SUBSTRATE PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,57914
Polyers129,2086
Non-polymers1,3718
Water2,918162
1
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
E: SUBSTRATE PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2897
Polyers64,6043
Non-polymers6864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2
F: SUBSTRATE PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2897
Polyers64,6043
Non-polymers6864
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)150.710, 164.100, 72.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2

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Components

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Protein/peptide , 3 types, 6 molecules ACBDEF

#1: Protein/peptide CELL DIVISION PROTEIN KINASE 2 / / P33 PROTEIN KINASE


Mass: 34143.547 Da / Num. of mol.: 2 / Details: PHOSPHORYLATED ON THR160 / Source: (gene. exp.) HOMO SAPIENS (human)
Description: CDK2 WAS CO-EXPRESSED WITH CAK1 - PRODUCE THR160-PHOSPHO-CDK2
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) PLYSS / References: UniProt: P24941
#2: Protein/peptide CYCLIN A2 /


Mass: 29624.297 Da / Num. of mol.: 2 / Fragment: RESIDUES 175-432 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) PLYSS / References: UniProt: P20248
#3: Protein/peptide SUBSTRATE PEPTIDE


Mass: 835.953 Da / Num. of mol.: 2 / Details: SEQUENCE HHASPRK / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 5 types, 170 molecules

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


Mass: 507.181 Da / Num. of mol.: 2 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Formula: NO3 / Nitrate
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Formula: C3H8O3 / Glycerol
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Formula: H2O / Water

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Details

Sequence detailsVAL B 175, N-TERMINAL DELETION OF RESIDUES 1-174 ENGINEERED IN EXPRESSION CONSTRUCT VAL D 175, ...VAL B 175, N-TERMINAL DELETION OF RESIDUES 1-174 ENGINEERED IN EXPRESSION CONSTRUCT VAL D 175, N-TERMINAL DELETION OF RESIDUES 1-174 ENGINEERED IN EXPRESSION CONSTRUCT MODRES: 1GY3 TPO A 160() THR160 HAS BEEN PHOSPHORYLATED BY COEXPRESSION WITH CAK1 MODRES: 1GY3 TPO C 160() THR160 HAS BEEN PHOSPHORYLATED BY COEXPRESSION WITH CAK1

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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: 3.3 / Density percent sol: 64.51 %
Crystal growpH: 7
Details: CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 4C FROM SOLUTIONS CONTAINING 10 MG/ML PCDK2/CYCLIN A, 100 MM HEPES PH7.0, 2 MM SUBSTRATE PEPTIDE, 1MM ADP, 1.0 M LI2SO4. CRYSTALS WERE TRANSFERRED TO 20%PEG 8K, 100 MM HEPES PH 7.0, 10 MM SUBSSTRATE PEPTIDE, 5 MM MG(NO3)2
Crystal grow
*PLUS
Temp: 4 ℃ / Method: vapor diffusion, sitting drop
components of the solutions
*PLUS

Crystal ID: 1 / Sol ID: drop

IDConcCommon nameDetailsChemical formula
110 mg/mlpCDK2/cyclinA
2100 mMHEPESpH7.0
32 mMpeptide
41 mMADP
51.05-1.15 MLi2SO4

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Type: ESRF BEAMLINE ID14-2 / Synchrotron site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionD resolution high: 2.7 Å / D resolution low: 2 Å / Number obs: 45572 / Rmerge I obs: 0.143 / NetI over sigmaI: 4.2 / Redundancy: 7 % / Percent possible obs: 84.4
Reflection shellRmerge I obs: 0.487 / Highest resolution: 2.7 Å / Lowest resolution: 2.81 Å / MeanI over sigI obs: 1.5 / Percent possible all: 40.7
Reflection
*PLUS
D resolution low: 2 Å / Number measured all: 319218
Reflection shell
*PLUS
Percent possible obs: 40.7

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Processing

Software
NameClassification
REFMACmodel building
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACphasing
REFMACrefinement
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QMZ
Overall SU ML: 0.39 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R Free: 0.42
Least-squares processR factor R free: 0.313 / R factor R work: 0.25 / Highest resolution: 2.7 Å / Lowest resolution: 2 Å / Number reflection obs: 41578 / Percent reflection R free: 5.1 / Percent reflection obs: 84.4
Refine hist #LASTHighest resolution: 2.7 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 9048 / Nucleic acid: 0 / Ligand: 76 / Solvent: 162 / Total: 9286
Least-squares process
*PLUS
R factor R work: 0.25 / R factor obs: 0.25 / Lowest resolution: 2 Å / Percent reflection R free: 5
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.020
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.0

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