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- PDB-2gvd: Complex Of Gs- With The Catalytic Domains Of Mammalian Adenylyl C... -

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Basic information

Entry
Database: PDB / ID: 2gvd
TitleComplex Of Gs- With The Catalytic Domains Of Mammalian Adenylyl Cyclase: Complex With TNP-ATP and Mn
Components
  • (Adenylate cyclase type ...) x 2
  • Guanine nucleotide-binding protein G(s), alpha subunit
KeywordsLYASE / ADENYLYL CYCLASE / GSA / TNP-ATP
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 / cAMP biosynthetic process / G alpha (z) signalling events / adenylate cyclase activity ...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 / cAMP biosynthetic process / G alpha (z) signalling events / adenylate cyclase activity / adenylate cyclase binding / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / D1 dopamine receptor binding / beta-2 adrenergic receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / cellular response to forskolin / adenylate cyclase activator activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cAMP-mediated signaling / ionotropic glutamate receptor binding / insulin-like growth factor receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating 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 / 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 / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / G-protein alpha subunit, group S / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-128 / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMou, T.-C. / Sprang, S.R.
CitationJournal: Mol.Pharmacol. / Year: 2006
Title: Broad specificity of Mammalian adenylyl cyclase for interaction with 2',3'-substituted purine- and pyrimidine nucleotide inhibitors.
Authors: Mou, T.-C. / Gille, A. / Suryanarayana, S. / Richter, M. / Seifert, R. / Sprang, S.R.
History
DepositionMay 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Sep 23, 2015Group: Non-polymer description
Revision 1.5Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.6Oct 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_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 1.7Aug 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), alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,02210
Polymers95,0133
Non-polymers2,0097
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.200, 133.400, 70.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-402-

HOH

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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, residues 440-657
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: ADCY5 / Plasmid: PQE60-H6-VC1(580) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / 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, residues 870-1081
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Adcy2 / Plasmid: PQE60-IIC2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / 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), alpha subunit / Adenylate cyclase-stimulating G alpha protein


Mass: 45769.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GNAS, GNAS1 / Plasmid: PQE60-H6-G(S)ALPHA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04896

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Non-polymers , 6 types, 58 molecules

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


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-FKP / METHYLPIPERAZINOFORSKOLIN


Mass: 550.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H50N2O7
#6: Chemical ChemComp-128 / SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE


Type: RNA linking / Mass: 718.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N8O19P3
#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.: 51 / 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: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 7.5-7.8% PEG8000, 0.5M NACL, 0.1M PHOSPHATE BUFFER, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 24, 2004 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.9→15 Å / Num. obs: 22450 / Redundancy: 4.3 % / Biso Wilson estimate: 53 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TL7

1tl7


Resolution: 2.9→14.96 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 264961.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 925 4.9 %RANDOM
Rwork0.245 ---
obs0.245 18842 82.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 16.3877 Å2 / ksol: 0.300325 e/Å3
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1--9.36 Å20 Å20 Å2
2---18.07 Å20 Å2
3---27.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.87 Å
Refinement stepCycle: LAST / Resolution: 2.9→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5586 0 121 51 5758
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.57
X-RAY DIFFRACTIONc_mcbond_it2.072
X-RAY DIFFRACTIONc_mcangle_it3.63
X-RAY DIFFRACTIONc_scbond_it3.243
X-RAY DIFFRACTIONc_scangle_it5.134
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 142 5.2 %
Rwork0.412 2568 -
obs--65.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2fkp.paramfkp.top
X-RAY DIFFRACTION3gsp.paramgsp.top
X-RAY DIFFRACTION4128.param128.top
X-RAY DIFFRACTION5water_rep.paramwater.top

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