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- PDB-7v0g: Structure of cAMP-dependent protein kinase using a MD-MX procedur... -

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Basic information

Entry
Database: PDB / ID: 7v0g
TitleStructure of cAMP-dependent protein kinase using a MD-MX procedure, produced using 1.63 Angstrom data
Components
  • Peptide from cAMP-dependent protein kinase inhibitor alpha
  • cAMP-dependent protein kinase catalytic subunit alphaCAMP-dependent pathway
KeywordsTRANSFERASE / protein kinase activity / cAMP-dependent protein kinase activity
Function / homology
Function and homology information


spontaneous exocytosis of neurotransmitter / HDL assembly / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion ...spontaneous exocytosis of neurotransmitter / HDL assembly / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / 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 / MAPK6/MAPK4 signaling / 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 / CD209 (DC-SIGN) signaling / negative regulation of cAMP-dependent protein kinase activity / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / RET signaling / Ion homeostasis / VEGFA-VEGFR2 Pathway / nucleotide-activated protein kinase complex / regulation of cellular respiration / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / axoneme / protein kinase A catalytic subunit binding / plasma membrane raft / mesoderm formation / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / protein kinase A signaling / positive regulation of gluconeogenesis / regulation of synaptic transmission, glutamatergic / negative regulation of TORC1 signaling / sperm midpiece / regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / modulation of chemical synaptic transmission / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / small GTPase binding / presynapse / cellular response to heat / manganese ion binding / postsynapse / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle / protein kinase activity / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / nucleus
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. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...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. / 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsWych, D.C. / Aoto, P.C. / Wall, M.E.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentUniversity of California Laboratory Fees Research Program (LFR-17-476732) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Molecular-dynamics simulation methods for macromolecular crystallography.
Authors: Wych, D.C. / Aoto, P.C. / Vu, L. / Wolff, A.M. / Mobley, D.L. / Fraser, J.S. / Taylor, S.S. / Wall, M.E.
History
DepositionMay 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: cAMP-dependent protein kinase catalytic subunit alpha
I: Peptide from cAMP-dependent protein kinase inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5147
Polymers42,8492
Non-polymers6665
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-48 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.976, 79.744, 99.058
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 2 molecules EI

#1: Protein cAMP-dependent protein kinase catalytic subunit alpha / CAMP-dependent pathway / 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
#2: Protein/peptide Peptide from cAMP-dependent protein kinase inhibitor alpha / / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 2111.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Residues 5-23 of the PKA-C inhibitor PKI / Source: (synth.) Homo sapiens (human) / References: UniProt: P61925

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Non-polymers , 4 types, 500 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 4000, 0.05 M MES pH 5.2, 0.05 M MgCl2, and 0.005 M DTT

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Data collection

DiffractionMean temperature: 285 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2018
Details: Primary Mirror: Flat; Secondary Mirror: uncooled cyllindrical silicon bent into torroid; 2:1 demagnification; Both mirrors coated with Pt/Rh
RadiationMonochromator: Water-cooled flat double Si(111) Khozu monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.63→47.42 Å / Num. obs: 58663 / % possible obs: 99.47 % / Redundancy: 4.6 % / Biso Wilson estimate: 19.77 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1056 / Rpim(I) all: 0.0534 / Rrim(I) all: 0.1188 / Net I/av σ(I): 7.39 / Net I/σ(I): 7.39
Reflection shellResolution: 1.63→1.688 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.374 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 5770 / CC1/2: 0.529 / CC star: 0.832 / Rpim(I) all: 0.6996 / Rrim(I) all: 0.1188 / % possible all: 99.79

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
DIALSdata reduction
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FJQ

3fjq


Resolution: 1.63→42.07 Å / SU ML: 0.1774 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.2502
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1625 1999 3.41 %
Rwork0.1163 56641 -
obs0.1179 58640 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.32 Å2
Refinement stepCycle: LAST / Resolution: 1.63→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 39 495 3392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833214
X-RAY DIFFRACTIONf_angle_d0.9944391
X-RAY DIFFRACTIONf_chiral_restr0.0549463
X-RAY DIFFRACTIONf_plane_restr0.0108562
X-RAY DIFFRACTIONf_dihedral_angle_d19.18941234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.670.30031400.22843974X-RAY DIFFRACTION99.78
1.67-1.720.29071410.21683998X-RAY DIFFRACTION99.66
1.72-1.770.22581420.20074005X-RAY DIFFRACTION99.5
1.77-1.820.25851420.17744006X-RAY DIFFRACTION99.86
1.82-1.890.22061410.1554012X-RAY DIFFRACTION99.83
1.89-1.960.16931420.12014022X-RAY DIFFRACTION99.83
1.96-2.050.17871420.10724051X-RAY DIFFRACTION99.71
2.05-2.160.15511430.09944028X-RAY DIFFRACTION99.57
2.16-2.30.14951420.09324037X-RAY DIFFRACTION99.62
2.3-2.470.15181420.09164041X-RAY DIFFRACTION99.67
2.47-2.720.151430.0994060X-RAY DIFFRACTION99.41
2.72-3.120.14871440.10574079X-RAY DIFFRACTION98.9
3.12-3.930.13521460.09894106X-RAY DIFFRACTION99.23
3.93-42.070.14531490.11834222X-RAY DIFFRACTION97.72

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