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- PDB-5hvz: Crystal structure of smAKAP AKB domain bound RIa dimerization/doc... -

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Basic information

Entry
Database: PDB / ID: 5hvz
TitleCrystal structure of smAKAP AKB domain bound RIa dimerization/docking (D/D) complex at 2.0 A resolution
Components
  • Small membrane A-kinase anchor protein
  • cAMP-dependent protein kinase type I-alpha regulatory subunit
KeywordsTRANSFERASE / A-kinase anchoring protein / small membrane AKAP / protein kinase A / regulatory subunit
Function / homology
Function and homology information


PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / PKA activation / Hedgehog 'off' state / sperm head-tail coupling apparatus / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity ...PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / PKA activation / Hedgehog 'off' state / sperm head-tail coupling apparatus / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / negative regulation of activated T cell proliferation / cAMP-dependent protein kinase complex / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / immunological synapse / plasma membrane raft / axoneme / cAMP binding / negative regulation of cAMP/PKA signal transduction / multivesicular body / cellular response to glucagon stimulus / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein domain specific binding / ubiquitin protein ligase binding / centrosome / glutamatergic synapse / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Small membrane A-kinase anchor protein / Small membrane A-kinase anchor protein / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / 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. ...Small membrane A-kinase anchor protein / Small membrane A-kinase anchor protein / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / 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. / 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 / RmlC-like jelly roll fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
cAMP-dependent protein kinase type I-alpha regulatory subunit / Small membrane A-kinase anchor protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWu, J. / Burgers, P.P. / Bruystens, J. / Heck, A.J.R. / Taylor, S.S.
Funding support Netherlands, United States, 2items
OrganizationGrant numberCountry
Netherlands Organization for Scientific Research262067 Netherlands
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK54441 United States
CitationJournal: Febs J. / Year: 2016
Title: Structure of smAKAP and its regulation by PKA-mediated phosphorylation.
Authors: Burgers, P.P. / Bruystens, J. / Burnley, R.J. / Nikolaev, V.O. / Keshwani, M. / Wu, J. / Janssen, B.J. / Taylor, S.S. / Heck, A.J. / Scholten, A.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP-dependent protein kinase type I-alpha regulatory subunit
B: cAMP-dependent protein kinase type I-alpha regulatory subunit
C: Small membrane A-kinase anchor protein


Theoretical massNumber of molelcules
Total (without water)14,8043
Polymers14,8043
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-53 kcal/mol
Surface area7000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.511, 55.737, 57.268
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 I-alpha regulatory subunit


Mass: 6005.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: PRKAR1A / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P00514
#2: Protein/peptide Small membrane A-kinase anchor protein / smAKAP


Mass: 2792.194 Da / Num. of mol.: 1 / Fragment: UNP Residues 56-79 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BSF0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.02 Å3/Da / Density % sol: 39.17 %
Crystal growTemperature: 297 K / Method: microbatch / pH: 3.5
Details: a 2:3 ratio of protein solution:crystallizing (crystallizing solution: 0.1 M Citric acid pH 3.5, 28% w/v Polyethylene glycol 8,000)
Temp details: room temperature

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Data collection

DiffractionMean temperature: 200 K / Ambient temp details: cryo under liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 8480 / % possible obs: 98 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.076 / Rsym value: 0.061 / Net I/σ(I): 26.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IM4

3im4


Resolution: 2→39.94 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.823 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.175 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24133 392 4.7 %RANDOM
Rwork0.20976 ---
obs0.21127 7937 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 30.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--0.65 Å20 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 2→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms959 0 0 29 988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022974
X-RAY DIFFRACTIONr_bond_other_d0.024
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.9881313
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4395117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18424.34846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.68215182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.253157
X-RAY DIFFRACTIONr_chiral_restr0.1510.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021717
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4371.5602
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6562959
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3453372
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.2584.5354
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: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 29 -
Rwork0.206 587 -
obs--99.84 %

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