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- PDB-3im4: Crystal structure of cAMP-dependent Protein Kinase A Regulatory S... -

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Basic information

Entry
Database: PDB / ID: 3im4
TitleCrystal structure of cAMP-dependent Protein Kinase A Regulatory Subunit I alpha in complex with dual-specific A-Kinase Anchoring Protein 2
Components
  • Dual specificity A kinase-anchoring protein 2
  • cAMP-dependent protein kinase type I-alpha regulatory subunitCAMP-dependent pathway
KeywordsSTRUCTURAL PROTEIN / SIGNALING PROTEIN / four-helix bundle / Acetylation / cAMP / cAMP-binding / Disulfide bond / Nucleotide-binding / Phosphoprotein / Cytoplasm / Membrane / Mitochondrion / Polymorphism / Transit peptide
Function / homology
Function and homology information


sperm connecting piece / 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 / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity ...sperm connecting piece / 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 / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / sarcomere organization / protein kinase A binding / cardiac muscle cell proliferation / cAMP-dependent protein kinase complex / Vasopressin regulates renal water homeostasis via Aquaporins / cellular response to glucagon stimulus / axoneme / negative regulation of activated T cell proliferation / protein kinase A catalytic subunit binding / plasma membrane raft / immunological synapse / mesoderm formation / cAMP binding / multivesicular body / regulation of protein phosphorylation / neuromuscular junction / protein localization / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / Factors involved in megakaryocyte development and platelet production / protein domain specific binding / negative regulation of gene expression / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / signal transduction / protein-containing complex / mitochondrion / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
A-kinase anchor protein 10, PKA-binding (AKB) domain / 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 / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain ...A-kinase anchor protein 10, PKA-binding (AKB) domain / 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 / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / 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
A-kinase anchor protein 10, mitochondrial / cAMP-dependent protein kinase type I-alpha regulatory subunit
Similarity search - Component
Biological speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.285 Å
AuthorsSarma, G.N. / Kinderman, F.S. / Kim, C. / von Daake, S. / Taylor, S.S.
CitationJournal: Structure / Year: 2010
Title: Structure of D-AKAP2:PKA RI Complex: Insights into AKAP Specificity and Selectivity
Authors: Sarma, G.N. / Kinderman, F.S. / Kim, C. / von Daake, S. / Chen, L. / Wang, B.C. / Taylor, S.S.
History
DepositionAug 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2022Group: 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Dual specificity A kinase-anchoring protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4268
Polymers17,0993
Non-polymers3275
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-52.9 kcal/mol
Surface area7460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.400, 56.020, 56.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL UNIT IS THE RI ALPHA DIMER BOUND TO A MONOMER OF D-AKAP2. AUTHOR STATES THAT THE QUARTERNARY STRUCTURE SHOWN IN REMARK 350 IS NOT CORRECT: IT IS *NOT* A TRIMER. IT IS A PROTEIN COMPLEX STRUCTURE OF TWO PROTEINS: A DIMER BOUND TO A MONOMER.

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Components

#1: Protein/peptide cAMP-dependent protein kinase type I-alpha regulatory subunit / CAMP-dependent pathway


Mass: 6005.980 Da / Num. of mol.: 2
Fragment: Dimerization and docking domain: UNP residues 13-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKAR1A / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00514
#2: Protein/peptide Dual specificity A kinase-anchoring protein 2 / Kinase anchor protein 10 / Protein kinase A-anchoring protein 10 / PRKA10 / D-AKAP-2


Mass: 5086.658 Da / Num. of mol.: 1 / Fragment: PKA-RII subunit binding: UNP residues 623-662
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKAP10 / Plasmid: pGEX 4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43572
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 1.89 Å3/Da / Density % sol: 34.78 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 5.5
Details: 10% PEG 6000, 0.01 M ZnCl2, 0.1 M MES, pH 5.5, MICROBATCH, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2008
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.285→50 Å / Num. obs: 6221 / % possible obs: 100 % / Observed criterion σ(I): 1
Reflection shellResolution: 2.285→2.38 Å / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.285→39.9567 Å / SU ML: 0.36 / σ(F): 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 600 9.98 %random
Rwork0.186 ---
all0.1927 6221 --
obs0.186 6015 96.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.871 Å2 / ksol: 0.329 e/Å3
Refinement stepCycle: LAST / Resolution: 2.285→39.9567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 5 30 1058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051040
X-RAY DIFFRACTIONf_angle_d0.811397
X-RAY DIFFRACTIONf_dihedral_angle_d17.216401
X-RAY DIFFRACTIONf_chiral_restr0.05157
X-RAY DIFFRACTIONf_plane_restr0.005181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.285-2.51520.29081360.20431240X-RAY DIFFRACTION91
2.5152-2.87910.311540.20391344X-RAY DIFFRACTION98
2.8791-3.62690.28711520.19691365X-RAY DIFFRACTION98
3.6269-39.95670.21531580.16821466X-RAY DIFFRACTION99
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined0.5158-0.4161-0.20090.9226-0.73541.1339-0.0118-0.0658-0.25640.06090.0179-0.23450.2213-0.0569-0.02230.1932-0.0124-0.00590.2240.020.3695-3.31620.0101-1.3816
20.6265-1.53440.5411.76471.2042.5814-0.1966-0.02340.2578-0.15410.14990.0433-0.5402-0.36580.01920.19710.0588-0.0110.17220.01510.3592
30.14230.31692.20992.1115-0.65997.9928-0.045-0.19280.1406-0.1281-0.29530.39690.3031-0.77670.27460.2881-0.0944-0.04150.42940.10950.6417
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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