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- PDB-1azs: COMPLEX OF GS-ALPHA WITH THE CATALYTIC DOMAINS OF MAMMALIAN ADENY... -

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Basic information

Entry
Database: PDB / ID: 1azs
TitleCOMPLEX OF GS-ALPHA WITH THE CATALYTIC DOMAINS OF MAMMALIAN ADENYLYL CYCLASE
Components
  • GS-ALPHA
  • IIC2
  • VC1
KeywordsCOMPLEX (LYASE/HYDROLASE) / COMPLEX (LYASE-HYDROLASE) / HYDROLASE / SIGNAL TRANSDUCING PROTEIN / CYCLASE / EFFECTOR ENZYME / COMPLEX (LYASE-HYDROLASE) 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 / cAMP biosynthetic process / corticotropin-releasing hormone receptor 1 binding ...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 / cAMP biosynthetic process / corticotropin-releasing hormone receptor 1 binding / 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 / ionotropic glutamate receptor binding / insulin-like growth factor 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
METHYLPIPERAZINOFORSKOLIN / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / 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: 2.3 Å
AuthorsTesmer, J.J.G. / Sprang, S.R.
CitationJournal: Science / Year: 1997
Title: Crystal structure of the catalytic domains of adenylyl cyclase in a complex with Gsalpha.GTPgammaS.
Authors: Tesmer, J.J. / Sunahara, R.K. / Gilman, A.G. / Sprang, S.R.
History
DepositionNov 20, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VC1
B: IIC2
C: GS-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5556
Polymers95,4403
Non-polymers1,1143
Water1,24369
1
A: VC1
B: IIC2
C: GS-ALPHA
hetero molecules

A: VC1
B: IIC2
C: GS-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,10912
Polymers190,8816
Non-polymers2,2296
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)119.000, 134.050, 70.650
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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Protein , 3 types, 3 molecules ABC

#1: Protein VC1


Mass: 25010.822 Da / Num. of mol.: 1 / Fragment: C1A DOMAIN OF ADENYLYL CYCLASE / Mutation: V476M, N-TERMINAL HEXAHISTIDINE TAG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Tissue: CARDIAC MUSCLE / Cellular location: PLASMA MEMBRANE / Gene: ADENYLYL CYCLASE TYPE V / Organ: PLASMA / Plasmid: PQE60-H6-VC1(580) / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): GNAS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P30803, adenylate cyclase
#2: Protein IIC2


Mass: 23717.033 Da / Num. of mol.: 1 / Fragment: C2A DOMAIN OF ADENYLYL CYCLASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: SPRAGUE-DAWLEY / Tissue: BRAIN / Cellular location: PLASMA MEMBRANE / Gene: ADENYLYL CYCLASE TYPE II / Organ: PLASMA / Plasmid: PQE60-ARGC-IIC2 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): GNAS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P26769, adenylate cyclase
#3: Protein GS-ALPHA / STIMULATORY G-PROTEIN ALPHA SUBUNIT


Mass: 46712.500 Da / Num. of mol.: 1
Mutation: C-TERMINAL HEXAHISTIDINE TAG, NOT PALMITOYLATED AT AMINO TERMINUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cellular location: CYTOPLASM AND INNER PLASMA MEMBRANE / Gene: GNAS / Organ: PLASMA / Variant: SHORT SPLICE FORM / Plasmid: PQE60-GSALPHA-H / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): GNAS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P04896

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Non-polymers , 4 types, 72 molecules

#4: Chemical ChemComp-FKP / METHYLPIPERAZINOFORSKOLIN


Mass: 550.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H50N2O7
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3 Å3/Da / Density % sol: 58 %
Description: DUE TO THE ANISOTROPIC DIFFRACTION, DATA WITH |L| 18 WERE DISCARDED PRIOR TO SCALING. INCLUDING THIS DATA, COMPLETENESS IS 96.7%, REDUNDANCY IS 3.1, RSYM IS 11.6%, AND AVERAGE I/SIGMA(I) ...Description: DUE TO THE ANISOTROPIC DIFFRACTION, DATA WITH |L| 18 WERE DISCARDED PRIOR TO SCALING. INCLUDING THIS DATA, COMPLETENESS IS 96.7%, REDUNDANCY IS 3.1, RSYM IS 11.6%, AND AVERAGE I/SIGMA(I) IS 8.6. AVERAGE I/SIGMA (I) FOR THE OMITTED REFLECTIONS (AFTER SCALING) IS 1.7.
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: CRYSTALLIZED IN HANGING DROPS CONTAINING PROTEIN MIXED 1:1 WITH WELL SOLUTION OF 7.2-7.5% PEG 8000, 500MM NACL AND 100 MM (PH 5.4-5.6), vapor diffusion - hanging drop
PH range: 5.4-5.6
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 5.6 / PH range high: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mMdithiothreitol1drop
20.200 mMMPFsk1drop
30.500 mMGTPgammaS1drop
48 mg/mlcomplex1drop
57.2-7.5 %PEG80001reservoir
6500 mM1reservoirNaCl
7100 mMMES1reservoirpH5.4-5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: ADSC / Detector: CCD / Date: Jun 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 37320 / % possible obs: 75.1 % / Observed criterion σ(I): -2 / Redundancy: 3.3 % / Biso Wilson estimate: 30.6 Å2 / Rsym value: 0.095 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.333 / % possible all: 46.6
Reflection
*PLUS
Num. all: 48048 / Rmerge(I) obs: 0.095

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GIA

1gia


Resolution: 2.3→15 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Details: A BULK SOLVENT CORRECTION WAS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 3752 7.4 %RANDOM
Rwork0.219 ---
obs0.219 37182 73.2 %-
Displacement parametersBiso mean: 52.2 Å2
Baniso -1Baniso -2Baniso -3
1--15.26 Å20 Å20 Å2
2---24.28 Å20 Å2
3---39.54 Å2
Refine analyzeLuzzati d res low obs: 15 Å / Luzzati sigma a obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5740 32 40 70 5882
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.88
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.41
X-RAY DIFFRACTIONx_mcangle_it5.3741.5
X-RAY DIFFRACTIONx_scbond_it4.3031
X-RAY DIFFRACTIONx_scangle_it6.7011.5
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.351 256 4.1 %
Rwork0.346 2328 -
obs--41.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION4FOK.PARFOK.TOP

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