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- PDB-8htg: Crystal structure of Golf in complex with GTP-gamma S and Mg -

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Basic information

Entry
Database: PDB / ID: 8htg
TitleCrystal structure of Golf in complex with GTP-gamma S and Mg
ComponentsGuanine nucleotide-binding protein G(olf) subunit alpha
KeywordsSIGNALING PROTEIN / G protein
Function / homology
Function and homology information


Adenylate cyclase activating pathway / Adenylate cyclase inhibitory pathway / Olfactory Signaling Pathway / cellular response to dopamine / response to caffeine / regulation of long-term synaptic depression / response to amphetamine / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway ...Adenylate cyclase activating pathway / Adenylate cyclase inhibitory pathway / Olfactory Signaling Pathway / cellular response to dopamine / response to caffeine / regulation of long-term synaptic depression / response to amphetamine / G protein-coupled 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 / adenylate cyclase-activating dopamine receptor signaling pathway / heterotrimeric G-protein complex / sensory perception of smell / G protein-coupled receptor signaling pathway / GTPase activity / GTP binding / metal ion binding / plasma membrane
Similarity search - Function
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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / PHOSPHATE ION / Guanine nucleotide-binding protein G(olf) subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsKang, H. / Choi, H.-J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Samsung Science and Technology FoundationSSTF-BA1901-09 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2023
Title: Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family.
Authors: Chulwon Choi / Jungnam Bae / Seonghan Kim / Seho Lee / Hyunook Kang / Jinuk Kim / Injin Bang / Kiheon Kim / Won-Ki Huh / Chaok Seok / Hahnbeom Park / Wonpil Im / Hee-Jung Choi /
Abstract: Structural and mechanistic studies on human odorant receptors (ORs), key in olfactory signaling, are challenging because of their low surface expression in heterologous cells. The recent structure of ...Structural and mechanistic studies on human odorant receptors (ORs), key in olfactory signaling, are challenging because of their low surface expression in heterologous cells. The recent structure of OR51E2 bound to propionate provided molecular insight into odorant recognition, but the lack of an inactive OR structure limited understanding of the activation mechanism of ORs upon odorant binding. Here, we determined the cryo-electron microscopy structures of consensus OR52 (OR52), a representative of the OR52 family, in the ligand-free (apo) and octanoate-bound states. The apo structure of OR52 reveals a large opening between transmembrane helices (TMs) 5 and 6. A comparison between the apo and active structures of OR52 demonstrates the inward and outward movements of the extracellular and intracellular segments of TM6, respectively. These results, combined with molecular dynamics simulations and signaling assays, shed light on the molecular mechanisms of odorant binding and activation of the OR52 family.
History
DepositionDec 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(olf) subunit alpha
B: Guanine nucleotide-binding protein G(olf) subunit alpha
C: Guanine nucleotide-binding protein G(olf) subunit alpha
D: Guanine nucleotide-binding protein G(olf) subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,93217
Polymers184,2694
Non-polymers2,66313
Water93752
1
A: Guanine nucleotide-binding protein G(olf) subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8836
Polymers46,0671
Non-polymers8165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-8 kcal/mol
Surface area16450 Å2
MethodPISA
2
B: Guanine nucleotide-binding protein G(olf) subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6934
Polymers46,0671
Non-polymers6263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-8 kcal/mol
Surface area16450 Å2
MethodPISA
3
C: Guanine nucleotide-binding protein G(olf) subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7264
Polymers46,0671
Non-polymers6593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-8 kcal/mol
Surface area16390 Å2
MethodPISA
4
D: Guanine nucleotide-binding protein G(olf) subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6313
Polymers46,0671
Non-polymers5642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-8 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.730, 52.360, 125.510
Angle α, β, γ (deg.)90.00, 118.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Guanine nucleotide-binding protein G(olf) subunit alpha / Adenylate cyclase-stimulating G alpha protein / olfactory type


Mass: 46067.273 Da / Num. of mol.: 4 / Mutation: C3S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gnal / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8CGK7

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Non-polymers , 5 types, 65 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.91 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 18% PEG 3350, 0.2M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.91→27.57 Å / Num. obs: 30932 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 43.54 Å2 / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.1779 / Rpim(I) all: 0.1122 / Rrim(I) all: 0.2108 / Net I/σ(I): 7.13
Reflection shellResolution: 2.91→3.01 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.8078 / Mean I/σ(I) obs: 1.48 / Num. unique obs: 3030 / CC1/2: 0.67 / CC star: 0.896 / Rpim(I) all: 0.5036 / Rrim(I) all: 0.9542 / % possible all: 99.84

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→27.57 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 1547 5 %
Rwork0.23 --
obs0.2318 30910 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.91→27.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10828 0 155 52 11035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211206
X-RAY DIFFRACTIONf_angle_d0.55115182
X-RAY DIFFRACTIONf_dihedral_angle_d10.184203
X-RAY DIFFRACTIONf_chiral_restr0.0431664
X-RAY DIFFRACTIONf_plane_restr0.0041944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-30.33241370.30862611X-RAY DIFFRACTION100
3-3.110.3551400.31692641X-RAY DIFFRACTION99
3.11-3.240.3581400.29732655X-RAY DIFFRACTION100
3.24-3.380.3661370.29492609X-RAY DIFFRACTION99
3.38-3.560.29281400.27312664X-RAY DIFFRACTION100
3.56-3.780.2681410.24292669X-RAY DIFFRACTION100
3.78-4.070.25711410.20172670X-RAY DIFFRACTION100
4.07-4.480.21991400.18752663X-RAY DIFFRACTION100
4.48-5.130.21261410.17442683X-RAY DIFFRACTION100
5.13-6.440.24581430.22232706X-RAY DIFFRACTION99
6.45-27.570.22511470.19292792X-RAY DIFFRACTION100

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