+Open data
-Basic information
Entry | Database: PDB / ID: 7ad3 | |||||||||
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Title | Class D GPCR Ste2 dimer coupled to two G proteins | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Fungal GPCR / Dimer / Complex / Class D / Active State | |||||||||
Function / homology | Function and homology information mating projection / : / protein localization to mating projection tip / PLC beta mediated events / G-protein activation / Acetylcholine regulates insulin secretion / G alpha (q) signalling events / ADP signalling through P2Y purinoceptor 1 / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / : ...mating projection / : / protein localization to mating projection tip / PLC beta mediated events / G-protein activation / Acetylcholine regulates insulin secretion / G alpha (q) signalling events / ADP signalling through P2Y purinoceptor 1 / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / : / G-protein beta/gamma-subunit complex / adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion / : / G alpha (12/13) signalling events / chemotropism / Cdc24p-Far1p-Gbetagamma complex / mating pheromone activity / mating-type factor pheromone receptor activity / nuclear migration involved in conjugation with cellular fusion / mating / G protein-coupled receptor homodimeric complex / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / karyogamy involved in conjugation with cellular fusion / G-protein gamma-subunit binding / establishment of protein localization to plasma membrane / invasive growth in response to glucose limitation / pheromone-dependent signal transduction involved in conjugation with cellular fusion / pheromone binding / cupric ion binding / G-protein alpha-subunit binding / cell periphery / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / small GTPase binding / G-protein beta-subunit binding / heterotrimeric G-protein complex / scaffold protein binding / endosome / endosome membrane / G protein-coupled receptor signaling pathway / GTPase activity / GTP binding / protein kinase binding / signal transduction / extracellular region / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Velazhahan, V. / Tate, C. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nature / Year: 2021 Title: Structure of the class D GPCR Ste2 dimer coupled to two G proteins. Authors: Vaithish Velazhahan / Ning Ma / Gáspár Pándy-Szekeres / Albert J Kooistra / Yang Lee / David E Gloriam / Nagarajan Vaidehi / Christopher G Tate / Abstract: G-protein-coupled receptors (GPCRs) are divided phylogenetically into six classes, denoted A to F. More than 370 structures of vertebrate GPCRs (belonging to classes A, B, C and F) have been ...G-protein-coupled receptors (GPCRs) are divided phylogenetically into six classes, denoted A to F. More than 370 structures of vertebrate GPCRs (belonging to classes A, B, C and F) have been determined, leading to a substantial understanding of their function. By contrast, there are no structures of class D GPCRs, which are found exclusively in fungi where they regulate survival and reproduction. Here we determine the structure of a class D GPCR, the Saccharomyces cerevisiae pheromone receptor Ste2, in an active state coupled to the heterotrimeric G protein Gpa1-Ste4-Ste18. Ste2 was purified as a homodimer coupled to two G proteins. The dimer interface of Ste2 is formed by the N terminus, the transmembrane helices H1, H2 and H7, and the first extracellular loop ECL1. We establish a class D1 generic residue numbering system (CD1) to enable comparisons with orthologues and with other GPCR classes. The structure of Ste2 bears similarities in overall topology to class A GPCRs, but the transmembrane helix H4 is shifted by more than 20 Å and the G-protein-binding site is a shallow groove rather than a cleft. The structure provides a template for the design of novel drugs to target fungal GPCRs, which could be used to treat numerous intractable fungal diseases. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ad3.cif.gz | 227.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ad3.ent.gz | 181.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ad3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ad3_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7ad3_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7ad3_validation.xml.gz | 44.6 KB | Display | |
Data in CIF | 7ad3_validation.cif.gz | 67.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/7ad3 ftp://data.pdbj.org/pub/pdb/validation_reports/ad/7ad3 | HTTPS FTP |
-Related structure data
Related structure data | 11720MC 7qa8C 7qb9C 7qbcC 7qbiC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10550 (Title: Structure of the class D GPCR Ste2 dimer coupled to two G proteins Data size: 6.4 TB / Data #1: LMB Krios1 Movies [micrographs - multiframe] / Data #2: LMB Krios2 Movies [micrographs - multiframe] / Data #3: eBic Krios1 Movies [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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-Components
-Protein , 2 types, 3 molecules BAF
#1: Protein | Mass: 47885.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: STE2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0CI39 #3: Protein | | Mass: 46626.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: STE4, GI526_G0005548 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A6A5Q727, UniProt: P18851*PLUS |
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-Guanine nucleotide-binding protein ... , 2 types, 3 molecules EHG
#4: Protein | Mass: 26316.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: GPA1, CDC70, DAC1, SCG1, YHR005C Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P08539 #5: Protein | | Mass: 12477.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: STE18, GI526_G0003318, PACBIOSEQ_LOCUS2168, PACBIOSEQ_LOCUS3627, PACBIOSEQ_LOCUS3692, PACBIOSEQ_LOCUS3742, PACBIOSEQ_LOCUS3767 Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A6A5PT44, UniProt: P18852*PLUS |
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-Protein/peptide / Sugars / Non-polymers , 3 types, 10 molecules KI
#2: Protein/peptide | Mass: 1685.986 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01149*PLUS #6: Sugar | #7: Chemical | ChemComp-Y01 / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 0.2667 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||
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Buffer solution | pH: 7.5 / Details: Solutions were made fresh and filtered | ||||||||||||||||||||||||||||||
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Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample was purified as a monodisperse complex | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company | ||||||||||||||||||||
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EM imaging | Accelerating voltage: 300 kV / Calibrated defocus max: 2700 nm / Calibrated defocus min: 900 nm / Cryogen: NITROGEN / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Model: FEI TITAN KRIOS / Mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2700 nm / Nominal defocus min: 900 nm / Temperature (max): 70 K / Temperature (min): 70 K / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen-ID: 1
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Image recording |
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EM imaging optics |
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-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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CTF correction |
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Particle selection |
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Symmetry |
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3D reconstruction | Entry-ID: 7AD3 / Resolution method: FSC 0.143 CUT-OFF / Symmetry type: POINT
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Atomic model building | B value: 112 / Space: REAL / Target criteria: Correlation coefficient Details: Manual building was performed in Coot iterated with real space refinement in PHENIX. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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