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- PDB-1fq1: CRYSTAL STRUCTURE OF KINASE ASSOCIATED PHOSPHATASE (KAP) IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 1fq1
TitleCRYSTAL STRUCTURE OF KINASE ASSOCIATED PHOSPHATASE (KAP) IN COMPLEX WITH PHOSPHO-CDK2
Components
  • CELL DIVISION PROTEIN KINASE 2
  • CYCLIN-DEPENDENT KINASE INHIBITOR 3
KeywordsHydrolase/Transferase / phospho-protein-protein complex / Hydrolase-Transferase COMPLEX
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / protein-serine/threonine phosphatase / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / regulation of heterochromatin organization / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase ...protein tyrosine/serine/threonine phosphatase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / protein-serine/threonine phosphatase / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / regulation of heterochromatin organization / 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 / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / protein serine/threonine phosphatase activity / 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 / 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 / Activation of ATR in response to replication stress / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin E associated events during G1/S transition / Cajal body / Cyclin A:Cdk2-associated events at S phase entry / Cyclin A/B1/B2 associated events during G2/M transition / cyclin-dependent protein kinase holoenzyme complex / regulation of G2/M transition of mitotic cell cycle / condensed chromosome / negative regulation of protein localization to chromatin / mitotic G1 DNA damage checkpoint signaling / protein-tyrosine-phosphatase / cellular response to nitric oxide / protein tyrosine phosphatase activity / post-translational protein modification / regulation of mitotic cell cycle / cyclin binding / positive regulation of DNA replication / male germ cell nucleus / meiotic cell cycle / potassium ion transport / peptidyl-serine phosphorylation / G1/S transition of mitotic cell cycle / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / G2/M transition of mitotic cell cycle / SCF(Skp2)-mediated degradation of p27/p21 / Transcriptional regulation of granulopoiesis / Orc1 removal from chromatin / Cyclin D associated events in G1 / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / regulation of gene expression / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / transcription regulator complex / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / protein phosphorylation / DNA replication / chromosome, telomeric region / endosome / regulation of cell cycle / chromatin remodeling / protein domain specific binding / negative regulation of cell population proliferation / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / positive regulation of cell population proliferation / centrosome / DNA-templated transcription / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / magnesium ion binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Cyclin-dependent kinase inhibitor 3 / CDKN3 domain / Cyclin-dependent kinase inhibitor 3 (CDKN3) / : / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / : / Protein-tyrosine phosphatase, catalytic ...Cyclin-dependent kinase inhibitor 3 / CDKN3 domain / Cyclin-dependent kinase inhibitor 3 (CDKN3) / : / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / : / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / 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 / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Cyclin-dependent kinase 2 / Cyclin-dependent kinase inhibitor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsSong, H. / Hanlon, N. / Brown, N.R. / Noble, M.E.M. / Johnson, L.N. / Barford, D.
Citation
Journal: Mol.Cell / Year: 2001
Title: Phosphoprotein-protein interactions revealed by the crystal structure of kinase-associated phosphatase in complex with phosphoCDK2.
Authors: Song, H. / Hanlon, N. / Brown, N.R. / Noble, M.E. / Johnson, L.N. / Barford, D.
#1: Journal: Science / Year: 1995
Title: Dephosphorylation of Cdk2 Thr160 by the cyclin dependent kinase-interacting phosphatase KAP in the absence of cyclin
Authors: Poon, R.Y.C. / Hunter, T.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: Cdi1, a human G1 and S phase protein phosphatase that associates with Cdk2
Authors: Gyruris, J. / Golemis, E. / Chertkov, H. / Brent, R.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: The p21Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases
Authors: Harper, J.W. / Adami, G.R. / Wei, N. / Keyomarsi, K. / Elledge, S.J.
History
DepositionSep 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 INHIBITOR 3
B: CELL DIVISION PROTEIN KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4074
Polymers57,8762
Non-polymers5312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-21 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.450, 134.450, 65.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CYCLIN-DEPENDENT KINASE INHIBITOR 3


Mass: 23819.057 Da / Num. of mol.: 1 / Mutation: C140S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HOMO SAPIENS / Production host: Escherichia coli (E. coli) / References: UniProt: Q16667, protein-tyrosine-phosphatase
#2: Protein CELL DIVISION PROTEIN KINASE 2


Mass: 34056.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HOMO SAPIENS / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has protein modificationY

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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: 2.96 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000,KCl, Mgacetate,Na cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
25 mgAMPPNP1drop
350 mMsodium cacodylate1reservoir
48-10 %(w/v)PEG80001reservoir
50.2 M1reservoirKCl
6100 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: ADSC / Detector: CCD / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 17091 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 95.5 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 5.6
Reflection shellResolution: 3→3.13 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.36 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 89741
Reflection shell
*PLUS
% possible obs: 99.6 % / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 3→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.313 702 -RANDOM
Rwork0.235 ---
obs-13940 99.7 %-
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 32 0 3854
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.8

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