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- PDB-1jsu: P27(KIP1)/CYCLIN A/CDK2 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1jsu
TitleP27(KIP1)/CYCLIN A/CDK2 COMPLEX
Components
  • CYCLIN A
  • CYCLIN-DEPENDENT KINASE-2
  • P27
KeywordsCOMPLEX (TRANSFERASE/CYCLIN/INHIBITOR) / COMPLEX (TRANSFERASE-CYCLIN-INHIBITOR) / KINASE / CELL CYCLE / CELL DIVISION / CDK / CYCLIN / INHIBITOR / COMPLEX (TRANSFERASE-CYCLIN-INHIBITOR) complex
Function / homology
Function and homology information


cyclin-dependent protein kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cyclin-dependent protein kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of kinase activity / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of epithelial cell proliferation involved in prostate gland development / negative regulation of cyclin-dependent protein serine/threonine kinase activity / : ...cyclin-dependent protein kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cyclin-dependent protein kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of kinase activity / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of epithelial cell proliferation involved in prostate gland development / negative regulation of cyclin-dependent protein serine/threonine kinase activity / : / cyclin A2-CDK1 complex / regulation of cell cycle G1/S phase transition / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / regulation of exit from mitosis / negative regulation of epithelial cell apoptotic process / epithelial cell proliferation involved in prostate gland development / cyclin-dependent protein serine/threonine kinase inhibitor activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / ubiquitin ligase activator activity / regulation of cyclin-dependent protein serine/threonine kinase activity / RHO GTPases activate CIT / male pronucleus / nuclear export / female pronucleus / negative regulation of mitotic cell cycle / cellular response to cocaine / AKT phosphorylates targets in the cytosol / epithelial cell apoptotic process / response to glucagon / positive regulation of DNA biosynthetic process / cellular response to antibiotic / cyclin-dependent protein serine/threonine kinase regulator activity / molecular function inhibitor activity / Cul4A-RING E3 ubiquitin ligase complex / cellular response to lithium ion / cellular response to insulin-like growth factor stimulus / 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 / Constitutive Signaling by AKT1 E17K in Cancer / PTK6 Regulates Cell Cycle / protein kinase inhibitor activity / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / inner ear development / 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 / regulation of G1/S transition of mitotic cell cycle / negative regulation of vascular associated smooth muscle cell proliferation / G0 and Early G1 / cochlea development / Telomere Extension By Telomerase / animal organ regeneration / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / 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 / Notch signaling pathway / mitotic G1 DNA damage checkpoint signaling / positive regulation of microtubule polymerization / FLT3 Signaling / cellular response to nitric oxide / post-translational protein modification / cyclin binding / regulation of mitotic cell cycle / regulation of cell migration / placenta development / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / DNA damage response, signal transduction by p53 class mediator / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / cellular response to estradiol stimulus / sensory perception of sound
Similarity search - Function
p27 / p27 / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : ...p27 / p27 / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / 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 / : / Few Secondary Structures / Irregular / 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 / Cyclin-dependent kinase inhibitor 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsRusso, A.A. / Jeffrey, P.D. / Pavletich, N.P.
CitationJournal: Nature / Year: 1996
Title: Crystal structure of the p27Kip1 cyclin-dependent-kinase inhibitor bound to the cyclin A-Cdk2 complex.
Authors: Russo, A.A. / Jeffrey, P.D. / Patten, A.K. / Massague, J. / Pavletich, N.P.
History
DepositionJul 3, 1996Processing site: BNL
Revision 1.0Jul 29, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: P27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9904
Polymers73,8943
Non-polymers961
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-61 kcal/mol
Surface area24400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.800, 78.300, 137.200
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.: 1 / Mutation: PHOSPHORYLATED AT THR A 160
Source method: isolated from a genetically manipulated source
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 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein CYCLIN A


Mass: 29867.512 Da / Num. of mol.: 1 / 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 WAS PRODUCED BY THE CLEAVAGE OF FULL-LENGTH CYCLIN A BY SUBTILISIN;
Cell line: SF9 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P20248
#3: Protein P27 / KIP1 / CIP2


Mass: 9970.153 Da / Num. of mol.: 1 / Fragment: RESIDUES 22 - 106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P46527
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
240 mMHEPES1drop
3200 mM1dropNaCl
45 mMdithiothreitol1drop
535 %satammonium sulfate1reservoir
640 mMHEPES1reservoir
75 mMdithiothreitol1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 20, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 162339 / % possible obs: 96.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.056
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 34683 / Num. measured all: 162339

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Processing

Software
NameClassification
TNTrefinement
HKLdata reduction
RefinementResolution: 2.3→7 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.26 --
Rwork0.192 --
obs-31351 96.1 %
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 5 197 5182
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg1.45
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_it3.6
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS

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