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- PDB-3c15: Complex of GS-Alpha with the Catalytic Domains of Mammalian Adeny... -

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Basic information

Entry
Database: PDB / ID: 3c15
TitleComplex of GS-Alpha with the Catalytic Domains of Mammalian Adenylyl Cyclase: Complex with Pyrophosphate and Mg
Components
  • (Adenylate cyclase type ...) x 2
  • Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
KeywordsLYASE/LYASE INHIBITOR / ADENYLYL CYCLASE / GSALPHA / PYROPHOSPHATE / MAGNESIUM / Alternative splicing / cAMP biosynthesis / Glycoprotein / Lyase / Membrane / Metal-binding / Phosphoprotein / Transmembrane / GTP-binding / Lipoprotein / Nucleotide-binding / Palmitate / Transducer / LYASE-LYASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Adenylate cyclase activating pathway / Hedgehog 'off' state / PKA activation / Adenylate cyclase inhibitory pathway / sensory perception of chemical stimulus / adenylate cyclase / regulation of insulin secretion involved in cellular response to glucose stimulus / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / cAMP biosynthetic process ...Adenylate cyclase activating pathway / Hedgehog 'off' state / PKA activation / Adenylate cyclase inhibitory pathway / sensory perception of chemical stimulus / adenylate cyclase / regulation of insulin secretion involved in cellular response to glucose stimulus / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / cAMP biosynthetic process / G alpha (z) signalling events / adenylate cyclase activity / beta-2 adrenergic receptor binding / adenylate cyclase binding / D1 dopamine receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / insulin-like growth factor receptor binding / cellular response to forskolin / adenylate cyclase activator activity / ionotropic glutamate receptor binding / cAMP-mediated signaling / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cilium / adenylate cyclase-activating dopamine receptor signaling pathway / heterotrimeric G-protein complex / manganese ion binding / positive regulation of cytosolic calcium ion concentration / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular signal transduction / membrane raft / GTPase activity / dendrite / GTP binding / magnesium ion binding / protein-containing complex / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Adenylate cyclase, conserved domain / Adenylate cyclase / Adenylate cyclase, N-terminal / Adenylate cyclase, conserved domain / Adenylyl cyclase N-terminal extracellular and transmembrane region / Nucleotide cyclase, GGDEF domain / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. ...Adenylate cyclase, conserved domain / Adenylate cyclase / Adenylate cyclase, N-terminal / Adenylate cyclase, conserved domain / Adenylyl cyclase N-terminal extracellular and transmembrane region / Nucleotide cyclase, GGDEF domain / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase / G-protein alpha subunit, group S / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORSKOLIN / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / PYROPHOSPHATE 2- / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Adenylate cyclase type 2 / Adenylate cyclase type 5
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
Rattus norvegicus (Norway rat)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsMou, T.-C. / Sprang, S.R.
CitationJournal: Biochemistry / Year: 2009
Title: Structural basis for inhibition of mammalian adenylyl cyclase by calcium.
Authors: Mou, T.C. / Masada, N. / Cooper, D.M. / Sprang, S.R.
History
DepositionJan 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: 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_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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 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

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Assembly

Deposited unit
A: Adenylate cyclase type 5
B: Adenylate cyclase type 2
C: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1428
Polymers95,9563
Non-polymers1,1855
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.510, 133.080, 70.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Adenylate cyclase type ... , 2 types, 2 molecules AB

#1: Protein Adenylate cyclase type 5 / Adenylate cyclase type V / ATP pyrophosphate-lyase 5 / Adenylyl cyclase 5 / Ca2+ / -inhibitable ...Adenylate cyclase type V / ATP pyrophosphate-lyase 5 / Adenylyl cyclase 5 / Ca2+ / -inhibitable adenylyl cyclase


Mass: 25526.514 Da / Num. of mol.: 1 / Fragment: C1A DOMAIN / Mutation: V476M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: ADCY5 / Plasmid: PQE60-H6-VC1(580) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P30803, adenylate cyclase
#2: Protein Adenylate cyclase type 2 / Adenylate cyclase type II / ATP pyrophosphate-lyase 2 / Adenylyl cyclase 2


Mass: 23717.033 Da / Num. of mol.: 1 / Fragment: C2A DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Adcy2 / Plasmid: PQE60-ARGC-IIC2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P26769, adenylate cyclase

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Protein , 1 types, 1 molecules C

#3: Protein Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Adenylate cyclase-stimulating G alpha protein


Mass: 46712.500 Da / Num. of mol.: 1 / Fragment: TRYPSINIZED FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GNAS, GNAS1 / Plasmid: PQE60-GSALPHA-H6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P04896

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Non-polymers , 6 types, 17 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-FOK / FORSKOLIN


Mass: 410.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H34O7
#6: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 7.5-7.8% PEG 8000, 0.5M NACL, 0.1M PHOSPHATE BUFFER, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0393 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 2004
Details: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0393 Å / Relative weight: 1
ReflectionResolution: 2.78→25 Å / Num. obs: 25942 / Redundancy: 3.1 % / Rsym value: 13.9
Reflection shellResolution: 2.78→2.9 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AZS

1azs


Resolution: 2.78→24.49 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.848 / SU B: 20.11 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R: 0.667 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29145 1250 5 %RANDOM
Rwork0.23704 ---
obs0.23981 23684 88.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.057 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.78→24.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5691 0 72 12 5775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225875
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9627959
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3195708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58524.105285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.78151023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0091539
X-RAY DIFFRACTIONr_chiral_restr0.0750.2885
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024404
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.22926
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24056
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2218
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1970.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.78→2.853 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 70 -
Rwork0.37 1328 -
obs--68.56 %

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