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- PDB-1l3r: Crystal Structure of a Transition State Mimic of the Catalytic Su... -

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Basic information

Entry
Database: PDB / ID: 1l3r
TitleCrystal Structure of a Transition State Mimic of the Catalytic Subunit of cAMP-dependent Protein Kinase
Components(CAMP-DEPENDENT PROTEIN ...) x 2
KeywordsTRANSFERASE / protein kinase / protein-ALF3 complex / transition state mimic
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 / negative regulation of catalytic activity / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling ...PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / DARPP-32 events / Rap1 signalling / negative regulation of catalytic activity / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Hedgehog 'off' state / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / MAPK6/MAPK4 signaling / negative regulation of cAMP-dependent protein kinase activity / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / GLI3 is processed to GLI3R by the proteasome / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / Interleukin-3, Interleukin-5 and GM-CSF signaling / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / CD209 (DC-SIGN) signaling / RET signaling / Regulation of PLK1 Activity at G2/M Transition / Mitochondrial protein degradation / VEGFA-VEGFR2 Pathway / Ion homeostasis / 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 / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus / regulation of osteoblast differentiation / cellular response to cold / 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 / intracellular potassium ion homeostasis / mesoderm formation / cAMP/PKA signal transduction / plasma membrane raft / axoneme / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / negative regulation of protein kinase activity / regulation of G2/M transition of mitotic cell cycle / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / sperm midpiece / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / positive regulation of gluconeogenesis / acrosomal vesicle / positive regulation of phagocytosis / protein export from nucleus / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / neuromuscular junction / cellular response to glucose stimulus / positive regulation of cholesterol biosynthetic process / positive regulation of insulin secretion / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / peptidyl-serine phosphorylation / modulation of chemical synaptic transmission / mRNA processing / adenylate cyclase-activating G protein-coupled receptor signaling pathway / manganese ion binding / cellular response to heat / protein kinase activity / postsynapse / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / centrosome / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / negative regulation of transcription by RNA polymerase II / 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'-DIPHOSPHATE / ALUMINUM FLUORIDE / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMadhusudan / Akamine, P. / Xuong, N.-H. / Taylor, S.S.
Citation
Journal: Nat.Struct.Biol. / Year: 2002
Title: Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase.
Authors: Madhusudan / Akamine, P. / Xuong, N.H. / Taylor, S.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: 2.0 A 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. / Ten Eyck, L.F. / Xuong, N. / Taylor, S.S. / Sowadski, J.M.
#2: 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. / Taylor, S.S. / Ten Eyck, L.F. / Sowadski, J.M.
#3: Journal: Protein Sci. / Year: 1994
Title: cAMP-dependent Protein Kinase: Crystallografic Insights into Substrate Recognition and Phosphotransfer
Authors: Madhusudan / Trafny, E.A. / Xuong, N.H. / Adams, J.A. / Ten Eyck, L.F. / Taylor, S.S. / Sowadski, J.M.
History
DepositionFeb 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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 / _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_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
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 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
E: CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT
I: CAMP-DEPENDENT PROTEIN KINASE INHIBITOR, MUSCLE/BRAIN FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6957
Polymers43,0172
Non-polymers6785
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-44 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.680, 75.700, 80.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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CAMP-DEPENDENT PROTEIN ... , 2 types, 2 molecules EI

#1: Protein CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT / PKA C-ALPHA


Mass: 40817.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, EC: 2.7.1.37
#2: Protein/peptide CAMP-DEPENDENT PROTEIN KINASE INHIBITOR, MUSCLE/BRAIN FORM / PKI-ALPHA


Mass: 2199.386 Da / Num. of mol.: 1 / Fragment: Residues 5-24 / Mutation: N20A, A21S / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus (mouse).
References: UniProt: P27776, UniProt: P63249*PLUS

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Non-polymers , 5 types, 238 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: MPD, bicine, methanol, ammonium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Details: Zheng, J.H., (1993) Acta Cryst., D49, 362.

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 12, 2000
RadiationMonochromator: 58 cm long, Pt-coated, fused silica, vertical focusmirror, Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. all: 30685 / Num. obs: 30443 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.068 / Net I/σ(I): 16.5
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.409 / % possible all: 95.8
Reflection
*PLUS
Lowest resolution: 35 Å / Num. measured all: 139545 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 95.8 % / Rmerge(I) obs: 0.408

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JBP

1jbp


Resolution: 2→35 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1819 -random
Rwork0.205 ---
all-30685 --
obs-30443 99.2 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.968 Å20 Å20 Å2
2---10.941 Å20 Å2
3---9.973 Å2
Refinement stepCycle: LAST / Resolution: 2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 33 241 3160
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shellResolution: 2→2.07 Å /
Rfactor% reflection
Rfree0.317 -
Rwork0.29 -
obs-95.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2PHOSPHO_RESI.param
X-RAY DIFFRACTION3dna-rna.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param
Refinement
*PLUS
Lowest resolution: 35 Å / σ(F): 0 / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.29

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