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- PDB-6au6: Crystal structure of GDP-bound human GNAS R201C mutant -

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Basic information

Entry
Database: PDB / ID: 6au6
TitleCrystal structure of GDP-bound human GNAS R201C mutant
ComponentsGuanine nucleotide-binding protein G(s) subunit alpha isoforms short
KeywordsSIGNALING PROTEIN / G protein / GDP / active conformation
Function / homology
Function and homology information


PKA activation in glucagon signalling / hair follicle placode formation / developmental growth / D1 dopamine receptor binding / intracellular transport / Hedgehog 'off' state / positive regulation of cAMP-mediated signaling / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / adenylate cyclase activator activity ...PKA activation in glucagon signalling / hair follicle placode formation / developmental growth / D1 dopamine receptor binding / intracellular transport / Hedgehog 'off' state / positive regulation of cAMP-mediated signaling / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / adenylate cyclase activator activity / trans-Golgi network membrane / G-protein beta/gamma-subunit complex binding / bone development / Prostacyclin signalling through prostacyclin receptor / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / platelet aggregation / cognition / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / positive regulation of GTPase activity / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / GPER1 signaling / heterotrimeric G-protein complex / sensory perception of smell / positive regulation of cold-induced thermogenesis / G alpha (i) signalling events / G alpha (s) signalling events / GTPase activity / GTP binding / extracellular exosome / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / 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 / P-loop containing nucleoside triphosphate hydrolase ...GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHu, Q. / Shokat, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Damon Runyon Cancer Research FoundationDRG-[2229-15] United States
CitationJournal: Cell / Year: 2018
Title: Disease-Causing Mutations in the G Protein G alpha s Subvert the Roles of GDP and GTP.
Authors: Hu, Q. / Shokat, K.M.
History
DepositionAug 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7086
Polymers44,0211
Non-polymers6875
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.370, 85.580, 125.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 44020.766 Da / Num. of mol.: 1 / Fragment: UNP residues 7-380 / Mutation: R201C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAS, GNAS1, GSP / Production host: Escherichia coli (E. coli) / References: UniProt: P63092

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Non-polymers , 5 types, 254 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.28 Å3/Da / Density % sol: 46.1 % / Description: long tube
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris 8.5, 25% PEG8000, 10 mM TCEP hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999907 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999907 Å / Relative weight: 1
ReflectionResolution: 1.7→62.82 Å / Num. obs: 44469 / % possible obs: 98.4 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Net I/σ(I): 12
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 6189 / Rpim(I) all: 0.149 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLM7.2.1data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AZT

1azt


Resolution: 1.7→33.042 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 19.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 2237 5.07 %
Rwork0.1684 --
obs0.1701 44154 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→33.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2807 0 42 249 3098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052913
X-RAY DIFFRACTIONf_angle_d0.8593937
X-RAY DIFFRACTIONf_dihedral_angle_d12.551742
X-RAY DIFFRACTIONf_chiral_restr0.048426
X-RAY DIFFRACTIONf_plane_restr0.004511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7370.23591230.21972460X-RAY DIFFRACTION95
1.737-1.77740.27411430.21162532X-RAY DIFFRACTION95
1.7774-1.82180.28621320.20482504X-RAY DIFFRACTION95
1.8218-1.87110.22151320.20022580X-RAY DIFFRACTION96
1.8711-1.92610.24391440.20122522X-RAY DIFFRACTION97
1.9261-1.98830.22941260.19092600X-RAY DIFFRACTION97
1.9883-2.05930.22071320.18452620X-RAY DIFFRACTION98
2.0593-2.14180.22611450.17672594X-RAY DIFFRACTION98
2.1418-2.23920.20971320.16812648X-RAY DIFFRACTION99
2.2392-2.35730.19241390.16332637X-RAY DIFFRACTION99
2.3573-2.50490.19621360.16552654X-RAY DIFFRACTION99
2.5049-2.69820.18231440.16982665X-RAY DIFFRACTION99
2.6982-2.96960.16181350.16922666X-RAY DIFFRACTION99
2.9696-3.39890.22481590.16522706X-RAY DIFFRACTION99
3.3989-4.28080.17011650.14522720X-RAY DIFFRACTION100
4.2808-33.04790.19161500.15712809X-RAY DIFFRACTION97

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