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- PDB-2izx: Molecular Basis of AKAP Specificity for PKA Regulatory Subunits -

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Basic information

Entry
Database: PDB / ID: 2izx
TitleMolecular Basis of AKAP Specificity for PKA Regulatory Subunits
Components
  • AKAP-IS
  • CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY SUBUNITCAMP-dependent pathway
KeywordsTRANSFERASE / CAMP-BINDING / PHOSPHORYLATION / NUCLEOTIDE-BINDING / PKA / CAMP / AKAP / ANCHOR / KINASE / ACETYLATION
Function / homology
Function and homology information


ROBO receptors bind AKAP5 / regulation of protein kinase A signaling / cAMP-dependent protein kinase regulator activity / nucleotide-activated protein kinase complex / PKA activation in glucagon signalling / negative regulation of cAMP-dependent protein kinase activity / PKA activation / CREB1 phosphorylation through the activation of Adenylate Cyclase / cAMP-dependent protein kinase inhibitor activity / regulation of cAMP-mediated signaling ...ROBO receptors bind AKAP5 / regulation of protein kinase A signaling / cAMP-dependent protein kinase regulator activity / nucleotide-activated protein kinase complex / PKA activation in glucagon signalling / negative regulation of cAMP-dependent protein kinase activity / PKA activation / CREB1 phosphorylation through the activation of Adenylate Cyclase / cAMP-dependent protein kinase inhibitor activity / regulation of cAMP-mediated signaling / cAMP-dependent protein kinase complex / Hedgehog 'off' state / ciliary base / DARPP-32 events / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cAMP binding / protein kinase A catalytic subunit binding / plasma membrane raft / ADORA2B mediated anti-inflammatory cytokines production / FCGR3A-mediated IL10 synthesis / Factors involved in megakaryocyte development and platelet production / intracellular signal transduction / centrosome / focal adhesion / protein domain specific binding / ubiquitin protein ligase binding / protein-containing complex / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / cAMP-dependent protein kinase regulatory subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain ...cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / cAMP-dependent protein kinase regulatory subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / 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-like / RmlC-like jelly roll fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DITHIANE DIOL / cAMP-dependent protein kinase type II-alpha regulatory subunit
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsGold, M.G. / Lygren, B. / Dokurno, P. / Hoshi, N. / McConnachie, G. / Tasken, K. / Carlson, C.R. / Scott, J.D. / Barford, D.
CitationJournal: Mol.Cell / Year: 2006
Title: Molecular Basis of Akap Specificity for Pka Regulatory Subunits.
Authors: Gold, M.G. / Lygren, B. / Dokurno, P. / Hoshi, N. / Mcconnachie, G. / Tasken, K. / Carlson, C.R. / Scott, J.D. / Barford, D.
History
DepositionJul 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY SUBUNIT
B: CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY SUBUNIT
C: AKAP-IS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9615
Polymers11,6563
Non-polymers3042
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)41.352, 45.251, 56.837
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY SUBUNIT / CAMP-dependent pathway / CAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT II


Mass: 4790.473 Da / Num. of mol.: 2 / Fragment: 3-43
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P13861, cAMP-dependent protein kinase
#2: Protein/peptide AKAP-IS


Mass: 2075.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growpH: 7.5 / Details: 1 M TRI-SODIUM CITRATE, 0.1 M TRIS-HCL PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 5, 2005 / Details: CYLINDRICAL GRAZING INCIDENCE MIRROR
RadiationMonochromator: SILICON FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.3→35.4 Å / Num. obs: 26863 / % possible obs: 99.7 % / Observed criterion σ(I): 2.5 / Redundancy: 4.35 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RII APO CRYSTAL STRUCTURE

Resolution: 1.3→28.42 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.469 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.Q4 IN AKAP-IS IS MODELLED AS ALANINE
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1348 5 %RANDOM
Rwork0.164 ---
obs0.166 25468 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.3→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms800 0 16 99 915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022828
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8052.0131122
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.787595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06424.04842
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.01215140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.621158
X-RAY DIFFRACTIONr_chiral_restr0.1440.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02620
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2780.2464
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.2593
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1671.5509
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7062800
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9273356
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5824.5322
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.353 105
Rwork0.316 1845

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