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- PDB-4x6q: An Isoform-specific Myristylation Switch Targets RIIb PKA Holoenz... -

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Basic information

Entry
Database: PDB / ID: 4x6q
TitleAn Isoform-specific Myristylation Switch Targets RIIb PKA Holoenzymes to Membranes
Components
  • cAMP-dependent protein kinase catalytic subunit alpha
  • cAMP-dependent protein kinase type II-beta regulatory subunit
KeywordsTRANSFERASE / PKA / membrane binding / molecular switch
Function / homology
Function and homology information


spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / positive regulation of triglyceride catabolic process / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion ...spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / positive regulation of triglyceride catabolic process / DARPP-32 events / Rap1 signalling / 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 / Anchoring of the basal body to the plasma membrane / Recruitment of NuMA to mitotic centrosomes / MAPK6/MAPK4 signaling / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / cAMP-dependent protein kinase regulator activity / GLI3 is processed to GLI3R by the proteasome / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / RET signaling / response to antipsychotic drug / Regulation of PLK1 Activity at G2/M Transition / Mitochondrial protein degradation / VEGFA-VEGFR2 Pathway / nucleotide-activated protein kinase complex / Ion homeostasis / regulation of cellular respiration / cAMP-dependent protein kinase inhibitor activity / histone H1-4S35 kinase activity / cAMP-dependent protein kinase / negative regulation of glycolytic process / regulation of protein processing / cAMP-dependent protein kinase activity / cellular response to parathyroid hormone stimulus / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / interleukin-2-mediated signaling pathway / regulation of osteoblast differentiation / sperm capacitation / cellular response to cold / ciliary base / protein kinase A regulatory subunit binding / negative regulation of glycolytic process through fructose-6-phosphate / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / mesoderm formation / TORC1 signaling / plasma membrane raft / axoneme / cAMP/PKA signal transduction / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / cAMP binding / negative regulation of cAMP/PKA signal transduction / regulation of synaptic transmission, glutamatergic / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / protein serine/threonine/tyrosine kinase activity / lipid droplet / cellular response to glucagon stimulus / positive regulation of phagocytosis / positive regulation of gluconeogenesis / cellular response to nutrient levels / acrosomal vesicle / positive regulation of protein export from nucleus / dendritic shaft / learning / negative regulation of smoothened signaling pathway / neural tube closure / neuromuscular junction / cellular response to glucose stimulus / fatty acid metabolic process / positive regulation of cholesterol biosynthetic process / modulation of chemical synaptic transmission / small GTPase binding / mRNA processing / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / manganese ion binding / cellular response to heat / adenylate cyclase-activating G protein-coupled receptor signaling pathway / presynapse / sperm midpiece / dendritic spine / protein kinase activity / regulation of cell cycle / nuclear speck / postsynapse / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain ...cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Jelly Rolls / 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 / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase type II-beta regulatory subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.52 Å
AuthorsZhang, P. / Ye, F. / Bastidas, A.C. / Kornev, A.P. / Ginsberg, M.H. / Taylor, S.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM034921 United States
CitationJournal: Structure / Year: 2015
Title: An Isoform-Specific Myristylation Switch Targets Type II PKA Holoenzymes to Membranes.
Authors: Zhang, P. / Ye, F. / Bastidas, A.C. / Kornev, A.P. / Wu, J. / Ginsberg, M.H. / Taylor, S.S.
History
DepositionDec 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Experimental preparation
Revision 1.2Sep 2, 2015Group: Database references
Revision 1.3Sep 16, 2015Group: Database references
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: cAMP-dependent protein kinase type II-beta regulatory subunit
C: cAMP-dependent protein kinase catalytic subunit alpha


Theoretical massNumber of molelcules
Total (without water)86,9312
Polymers86,9312
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-14 kcal/mol
Surface area28880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.714, 214.039, 61.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein cAMP-dependent protein kinase type II-beta regulatory subunit


Mass: 46193.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkar2b / Production host: Escherichia coli (E. coli) / References: UniProt: P31324
#2: Protein cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha


Mass: 40737.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkaca, Pkaca / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, cAMP-dependent protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 298 K / Method: batch mode
Details: The RIIb(R230K)2: myrC(K7C)2 holoenzyme was concentrated to 12 mg/mL. The crystal used for structure determination was obtained from a 3 uL drop containing 1:1 protein to well solution with ...Details: The RIIb(R230K)2: myrC(K7C)2 holoenzyme was concentrated to 12 mg/mL. The crystal used for structure determination was obtained from a 3 uL drop containing 1:1 protein to well solution with the well solution containing 10% PEG8000, 8% ethylene glycol, 20mM MES, at pH5.8.

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jul 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.52→44 Å / Num. obs: 31571 / % possible obs: 95.26 % / Redundancy: 3 % / Net I/σ(I): 24

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.52→43.821 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 1660 5 %
Rwork0.1983 --
obs0.2014 -95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→43.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4919 0 0 76 4995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115020
X-RAY DIFFRACTIONf_angle_d1.3486765
X-RAY DIFFRACTIONf_dihedral_angle_d16.8261890
X-RAY DIFFRACTIONf_chiral_restr0.053728
X-RAY DIFFRACTIONf_plane_restr0.006870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5186-2.59270.39111230.28852303X-RAY DIFFRACTION84
2.5927-2.67640.32671460.27872648X-RAY DIFFRACTION98
2.6764-2.7720.34871250.26462673X-RAY DIFFRACTION98
2.772-2.8830.36661220.25292677X-RAY DIFFRACTION98
2.883-3.01420.33191490.25172687X-RAY DIFFRACTION98
3.0142-3.17310.3871460.25362675X-RAY DIFFRACTION98
3.1731-3.37180.28991390.23642680X-RAY DIFFRACTION98
3.3718-3.6320.27711420.2292653X-RAY DIFFRACTION97
3.632-3.99730.26491460.19932568X-RAY DIFFRACTION94
3.9973-4.57520.2211310.16122643X-RAY DIFFRACTION95
4.5752-5.76220.21981460.16092641X-RAY DIFFRACTION94
5.7622-43.82740.19511450.15492723X-RAY DIFFRACTION93

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