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- PDB-1azt: GS-ALPHA COMPLEXED WITH GTP-GAMMA-S -

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Basic information

Entry
Database: PDB / ID: 1azt
TitleGS-ALPHA COMPLEXED WITH GTP-GAMMA-S
ComponentsGS-ALPHA
KeywordsHYDROLASE / SIGNAL TRANSDUCING PROTEIN / GTP-BINDING PROTEIN
Function / homology
Function and homology information


sensory perception of chemical stimulus / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / beta-2 adrenergic receptor binding / D1 dopamine receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / insulin-like growth factor receptor binding / ionotropic glutamate receptor binding / adenylate cyclase activator activity / G-protein beta/gamma-subunit complex binding ...sensory perception of chemical stimulus / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / beta-2 adrenergic receptor binding / D1 dopamine receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / insulin-like growth factor receptor binding / ionotropic glutamate receptor binding / adenylate cyclase activator activity / 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / 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 / Rossmann fold ...GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / PHOSPHATE ION / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Similarity search - Component
Biological speciesBos 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 adenylyl cyclase activator Gsalpha
Authors: Sunahara, R.K. / Tesmer, J.J. / 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 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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: GS-ALPHA
B: GS-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,07222
Polymers93,4252
Non-polymers2,64720
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-154 kcal/mol
Surface area30930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.300, 96.500, 133.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9999, -0.0113, -0.0105), (-0.0114, -0.9999, -0.0098), (-0.0104, 0.0099, -0.9999)
Vector: 0.4034, 48.3911, 33.2359)

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Components

#1: Protein GS-ALPHA / STIMULATORY G-PROTEIN ALPHA SUBUNIT


Mass: 46712.500 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDATABASE ENTRY IS FOR THE LONG SPLICE VARIANT. RESIDUES 71-84 ARE SPLICED OUT IN THE SHORT SPLICE ...DATABASE ENTRY IS FOR THE LONG SPLICE VARIANT. RESIDUES 71-84 ARE SPLICED OUT IN THE SHORT SPLICE VARIANT USED IN THIS EXPERIMENT. SEQUENCE NUMBERS REFLECT THOSE OF THE LONG SPLICE VARIANT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5
Details: CRYSTALLIZED IN HANGING DROPS CONTAINING PROTEIN MIXED 1:1 WITH WELL SOLUTION CONSISTING OF 90-100% SATURATED KH2PO4 OR NAH2PO4 (UNBUFFERED)., pH 4.5, vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 mg/mlGsalpha1drop
20.8 mMGTPgammaS1drop
320 mMsodium HEPES1drop
45 mM1dropMgCl2
51 mMEDTA1drop
65 mMdithiothreitol1drop
790-100 %satpotassium phosphate1reservoircan be replaced by 2.5M sodium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: ADSC QUANTUM / 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: 2.5 Å / Num. obs: 37636 / % possible obs: 94 % / Observed criterion σ(I): -2 / Redundancy: 4.2 % / Biso Wilson estimate: 30.6 Å2 / Rsym value: 0.138 / Net I/σ(I): 8.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.417 / % possible all: 95.1
Reflection
*PLUS
Rmerge(I) obs: 0.138

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
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: 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. atoms5560 0 146 57 5763
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.88

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