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- PDB-3g82: Complex of GS-alpha with the catalytic domains of mammalian adeny... -

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Basic information

Entry
Database: PDB / ID: 3g82
TitleComplex of GS-alpha with the catalytic domains of mammalian adenylyl cyclase: complex with MANT-ITP and Mn
Components
  • (Adenylate cyclase type ...) x 2
  • Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
KeywordsLyase/Lyase Inhibitor / ADENYLYL CYCLASE / MANT-ITP / Alternative splicing / cAMP biosynthesis / Glycoprotein / Lyase / Magnesium / Membrane / Metal-binding / Phosphoprotein / Transmembrane / Cell membrane / 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 / adenylate cyclase / sensory perception of chemical stimulus / regulation of insulin secretion involved in cellular response to glucose stimulus / mu-type opioid receptor binding / cAMP biosynthetic process / corticotropin-releasing hormone receptor 1 binding ...Adenylate cyclase activating pathway / Hedgehog 'off' state / PKA activation / Adenylate cyclase inhibitory pathway / adenylate cyclase / sensory perception of chemical stimulus / regulation of insulin secretion involved in cellular response to glucose stimulus / mu-type opioid receptor binding / cAMP biosynthetic process / corticotropin-releasing hormone receptor 1 binding / adenylate cyclase activity / G alpha (z) signalling events / 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 / ionotropic glutamate receptor binding / cellular response to forskolin / adenylate cyclase activator activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / cilium / membrane raft / GTPase activity / dendrite / GTP binding / magnesium ion binding / protein-containing complex / ATP binding / metal ion binding / membrane / 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 / Chem-MI3 / : / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsHuebner, M. / Mou, T.-C. / Sprang, S.R. / Seifert, R.
CitationJournal: To be Published
Title: 2',3'-(O)-(N-Methyl)anthraniloyl-inosine 5'-triphosphate is the Most Potent Adenylyl Cyclase 1 and 5 Inhibitor Known so far and Effectively Promotes Catalytic Subunit Assembly in the Absence of Forskolin
Authors: Huebner, M. / Geduhn, J. / Pinto, C. / Mou, T.-C. / Konig, B. / Sprang, S.R. / Seifert, R.
History
DepositionFeb 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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
Revision 1.3Sep 6, 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
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)96,77410
Polymers95,0133
Non-polymers1,7617
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-67 kcal/mol
Surface area31290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.637, 133.423, 70.642
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 / Ca(2+)-inhibitable ...Adenylate cyclase type V / ATP pyrophosphate-lyase 5 / Adenylyl cyclase 5 / Ca(2+)-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) / Strain: HEART / Gene: ADCY5 / Plasmid: PQE60-H6-VC1(580) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / 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) / Strain: BRAIN / Gene: Adcy2 / Plasmid: PQE60-ARGC-IIC2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / 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: 45769.527 Da / Num. of mol.: 1 / Fragment: TRYPSINIZED FRAGMENT OF G(S)ALPHA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Strain: NOSTRIL / Gene: GNAS, GNAS1 / Plasmid: PQE60-GSALPHA-H6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P04896

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Non-polymers , 7 types, 11 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-FOK / FORSKOLIN


Mass: 410.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H34O7
#6: Chemical ChemComp-MI3 / 3'-O-{[2-(methylamino)phenyl]carbonyl}inosine 5'-(tetrahydrogen triphosphate)


Mass: 641.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N5O15P3
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CL / CHLORIDE ION


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


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


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 7.2-7.8% PEG8000, 0.5M NACL, 0.1M 2-morpholinoethanesulfonic acid, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2008
Details: Vertical focusing mirror, single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: Si(311)BENT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.11→15 Å / Num. all: 16674 / Num. obs: 16244 / Redundancy: 3 % / Rsym value: 0.179
Reflection shellResolution: 3.11→3.21 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.345

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TL7

1tl7


Resolution: 3.11→15 Å / Cor.coef. Fo:Fc: 0.852 / Cor.coef. Fo:Fc free: 0.711 / SU B: 26.837 / SU ML: 0.468 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / ESU R Free: 0.622 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29376 847 5.1 %RANDOM
Rwork0.23688 ---
obs0.24028 15822 81.36 %-
all-16244 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.183 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 3.11→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5645 0 106 4 5755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0225864
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0421.9717949
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.335703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49724.128281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.474151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2471538
X-RAY DIFFRACTIONr_chiral_restr0.0730.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214385
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.22864
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.24040
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2211
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.4250.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.22
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: 3.11→3.183 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 47 -
Rwork0.307 732 -
obs--53.69 %

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