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- PDB-1atp: 2.2 angstrom refined crystal structure of the catalytic subunit o... -

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Basic information

Entry
Database: PDB / ID: 1atp
Title2.2 angstrom refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MNATP and a peptide inhibitor
Components
  • PEPTIDE INHIBITOR PKI(5-24)
  • cAMP-DEPENDENT PROTEIN KINASE
KeywordsTRANSFERASE(PHOSPHOTRANSFERASE)
Function / homology
Function and homology information


PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / Hedgehog 'off' state ...PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / Hedgehog 'off' state / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / RET signaling / Mitochondrial protein degradation / Ion homeostasis / VEGFA-VEGFR2 Pathway / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / cAMP/PKA signal transduction / sperm flagellum / plasma membrane raft / axoneme / postsynaptic modulation of chemical synaptic transmission / regulation of G2/M transition of mitotic cell cycle / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / sperm midpiece / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / positive regulation of cholesterol biosynthetic process / modulation of chemical synaptic transmission / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / peptidyl-serine phosphorylation / manganese ion binding / cellular response to heat / postsynapse / protein kinase activity / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / magnesium ion binding / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
ADENOSINE-5'-TRIPHOSPHATE / : / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsZheng, J. / Trafny, E.A. / Knighton, D.R. / Xuong, N.-H. / Taylor, S.S. / Teneyck, L.F. / Sowadski, J.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: 2.2 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor.
Authors: Zheng, J. / Trafny, E.A. / Knighton, D.R. / Xuong, N.H. / Taylor, S.S. / Ten Eyck, L.F. / Sowadski, J.M.
#1: Journal: To be Published
Title: 2.0 Angstrom Refined Crystal Structure of the Catalytic Subunit of Camp-Dependent Protein Kinase Complexed with a Peptide Inhibitor and Detergent
Authors: Knighton, D.R. / Bell, S.M. / Zheng, J. / Teneyck, L.F. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M.
#2: Journal: Biochemistry / Year: 1993
Title: Crystal Structure of the Catalytic Subunit of cAMP-Dependent Protein Kinase Complexed with Mg/ATP and Peptide Inhibitor
Authors: Zheng, J. / Knighton, D.R. / Teneyck, L.F. / Karlsson, R. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M.
#3: Journal: Science / Year: 1991
Title: Crystal Structure of the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase
Authors: Knighton, D.R. / Zheng, J. / Teneyck, L.F. / Xuong, V.A. / Ashford, N.-H. / Taylor, S.S. / Sowadski, J.M.
#4: Journal: Science / Year: 1991
Title: Structure of a Peptide Inhibitor Bound to the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase
Authors: Knighton, D.R. / Zheng, J. / Teneyck, L.F. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M.
#5: Journal: J.Biol.Chem. / Year: 1989
Title: Expression of the Catalytic Subunit of C/AMP-Dependent Protein Kinase in Escherichia Coli
Authors: Slice, L.W. / Taylor, S.S.
History
DepositionJan 8, 1993Processing site: BNL
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / software / struct_conn
Item: _pdbx_database_status.process_site / _software.classification / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Nov 6, 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_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _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_conn_type.id / _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

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Assembly

Deposited unit
E: cAMP-DEPENDENT PROTEIN KINASE
I: PEPTIDE INHIBITOR PKI(5-24)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5015
Polymers42,8842
Non-polymers6173
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-14 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.580, 76.280, 80.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES THR E 197 AND SER E 338 ARE PHOSPHORYLATED.

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Components

#1: Protein cAMP-DEPENDENT PROTEIN KINASE


Mass: 40657.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P05132, EC: 2.7.1.37
#2: Protein/peptide PEPTIDE INHIBITOR PKI(5-24)


Mass: 2226.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P63248
#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.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsINHIBITOR RESIDUE NUMBERING CORRESPONDS TO NUMBERS FROM THE SEQUENCE OF THE LARGER NATURALLY ...INHIBITOR RESIDUE NUMBERING CORRESPONDS TO NUMBERS FROM THE SEQUENCE OF THE LARGER NATURALLY OCCURRING PKI PROTEIN OF WHICH THE INHIBITOR IS A SYNTHETIC FRAGMENT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Zheng, J., (1993) Biochemistry, 32, 2154.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250 mMBicine1drop
3150 mMammonium acetate1drop
410 mMdithiothreitol1drop
58 %(w/v)PEG4001drop
610 mMdithiothreitol1reservoir
78 %(w/v)PEG4001reservoir
815 %methanol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 21443 / % possible obs: 90.6 % / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.37 Å / Rmerge(I) obs: 0.079

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→10 Å / Rfactor Rwork: 0.177 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 33 103 3070
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg2.2
Software
*PLUS
Name: XPLOR/TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.199 / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_bond_d
X-RAY DIFFRACTIONt_angle_deg

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