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- PDB-1jst: PHOSPHORYLATED CYCLIN-DEPENDENT KINASE-2 BOUND TO CYCLIN A -

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Basic information

Entry
Database: PDB / ID: 1jst
TitlePHOSPHORYLATED CYCLIN-DEPENDENT KINASE-2 BOUND TO CYCLIN A
Components
  • CYCLIN A
  • CYCLIN-DEPENDENT KINASE-2
KeywordsCOMPLEX (PROTEIN KINASE/CYCLIN) / COMPLEX (PROTEIN KINASE-CYCLIN) / CYCLIN / CDK / PHOSPHORYLATION / COMPLEX (PROTEIN KINASE-CYCLIN) complex
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 / cellular response to leptin stimulus / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / 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 / cellular response to leptin stimulus / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / male pronucleus / female pronucleus / cellular response to cocaine / 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 / 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 / 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 anaphase-promoting complex-dependent catabolic process / cellular response to platelet-derived growth factor stimulus / regulation of DNA replication / 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 / G0 and Early G1 / Telomere Extension By Telomerase / cellular response to nitric oxide / Activation of the pre-replicative complex / animal organ regeneration / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / 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 / mitotic G1 DNA damage checkpoint signaling / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / 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 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / G1/S transition of mitotic cell cycle / 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) / peptidyl-serine phosphorylation / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / DNA replication / chromosome, telomeric region / Ub-specific processing proteases / endosome / chromatin remodeling / protein phosphorylation / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation / protein kinase 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, C-terminal domain / Cyclin_C / Cyclin-like ...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 / : / 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. / 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
ADENOSINE-5'-TRIPHOSPHATE / : / Cyclin-A2 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsRusso, A.A. / Jeffrey, P.D. / Pavletich, N.P.
CitationJournal: Nat.Struct.Biol. / Year: 1996
Title: Structural basis of cyclin-dependent kinase activation by phosphorylation.
Authors: Russo, A.A. / Jeffrey, P.D. / Pavletich, N.P.
History
DepositionJul 3, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 A
C: CYCLIN-DEPENDENT KINASE-2
D: CYCLIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4868
Polymers127,3624
Non-polymers1,1244
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: CYCLIN-DEPENDENT KINASE-2
B: CYCLIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2434
Polymers63,6812
Non-polymers5622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-25 kcal/mol
Surface area22210 Å2
MethodPISA
3
C: CYCLIN-DEPENDENT KINASE-2
D: CYCLIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2434
Polymers63,6812
Non-polymers5622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-26 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.600, 149.100, 74.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYCLIN-DEPENDENT KINASE-2 / CDK2


Mass: 34056.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATED / Source: (gene. exp.) Homo sapiens (human)
Description: CYCLIN A-BOUND FORM PHOSPHORYLATED ON THR 160 IN VITRO USING A CDK-ACTIVATING KINASE CONSISTING OF THE CYCLINH-CDK7 COMPLEX;
Cell line: SF9 / Plasmid: PET3A / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein CYCLIN A


Mass: 29624.297 Da / Num. of mol.: 2 / Fragment: RESIDUES 173-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: THE FRAGMENT USED IN THE CRYSTALLIZATION (RESIDUES 173-432) WAS PRODUCED BY THE CLEAVAGE OF FULL-LENGTH CYCLIN A BY SUBTILISIN
Cell line: SF9 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): SF9 / References: UniProt: P20248
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Jeffrey, P.D., (1995) Nature, 376, 313.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlCDK2 and cyclinA fragment1drop
240 mMHEPES1drop
30.2 M1dropNaCl
45 mMDTT1drop
528 %sat1reservoir(NH4)2SO4
61 M1reservoirKCl
740 mMHEPES1reservoir
85 mMDTT1reservoir
910 mMATP1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92
DetectorDetector: CCD / Date: Dec 22, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
Reflection% possible obs: 98.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.066
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. obs: 48448 / Num. measured all: 290942

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Processing

Software
NameClassification
TNTrefinement
HKLdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.6→7 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.2 --
obs-39189 98.9 %
Refinement stepCycle: LAST / Resolution: 2.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8972 0 64 98 9134
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg1.74
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it2.7
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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