+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11720 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Class D GPCR Ste2 dimer coupled to two G proteins | |||||||||
Map data | Map1 | |||||||||
Sample |
| |||||||||
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 ...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 / adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion / G-protein beta/gamma-subunit complex / 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 / pheromone-dependent signal transduction involved in conjugation with cellular fusion / invasive growth in response to glucose limitation / pheromone binding / cupric ion binding / G-protein alpha-subunit binding / G-protein beta/gamma-subunit complex binding / cell periphery / G protein-coupled receptor binding / small GTPase binding / G-protein beta-subunit binding / heterotrimeric G-protein complex / scaffold protein binding / endosome membrane / endosome / G protein-coupled receptor signaling pathway / GTPase activity / GTP binding / protein kinase binding / signal transduction / extracellular region / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Velazhahan V / Tate C | |||||||||
Funding support | United Kingdom, 2 items
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11720.map.gz | 3.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11720-v30.xml emd-11720.xml | 39.6 KB 39.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11720_fsc.xml | 7.5 KB | Display | FSC data file |
Images | emd_11720.png | 124.3 KB | ||
Others | emd_11720_additional_1.map.gz emd_11720_half_map_1.map.gz emd_11720_half_map_2.map.gz | 2.2 MB 27.2 MB 27.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11720 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11720 | HTTPS FTP |
-Validation report
Summary document | emd_11720_validation.pdf.gz | 399.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_11720_full_validation.pdf.gz | 398.8 KB | Display | |
Data in XML | emd_11720_validation.xml.gz | 13 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11720 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11720 | HTTPS FTP |
-Related structure data
Related structure data | 7ad3MC 7qa8C 7qb9C 7qbcC 7qbiC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
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
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_11720.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Map1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.047 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: Map2
File | emd_11720_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Map2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Halfmap1 for calculating map1
File | emd_11720_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Halfmap1 for calculating map1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Halfmap2 for calculating map1
File | emd_11720_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Halfmap2 for calculating map1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Ste2 dimer coupled to two G proteins
+Supramolecule #1: Ste2 dimer coupled to two G proteins
+Supramolecule #2: Ste2 dimer coupled to two G proteins
+Supramolecule #3: Alpha-factor mating pheromone
+Supramolecule #4: Guanine nucleotide-binding protein alpha-1 subunit,Guanine nucleo...
+Macromolecule #1: Pheromone alpha factor receptor
+Macromolecule #2: Alpha-factor mating pheromone
+Macromolecule #3: STE4 isoform 1
+Macromolecule #4: Guanine nucleotide-binding protein alpha-1 subunit,Guanine nucleo...
+Macromolecule #5: Guanine nucleotide-binding protein subunit gamma
+Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #7: CHOLESTEROL HEMISUCCINATE
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
Details: Solutions were made fresh and filtered | ||||||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||
Details | The sample was purified as a monodisperse complex |
-Electron microscopy #1
Microscopy ID | 1 |
---|---|
Microscope | FEI TITAN KRIOS |
Temperature | Min: 70.0 K / Max: 70.0 K |
Specialist optics | Energy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV |
Details | eBIC Krios1 |
Image recording | Image recording ID: 1 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.7 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Electron microscopy #1~
Microscopy ID | 1 |
---|---|
Microscope | FEI TITAN KRIOS |
Temperature | Min: 70.0 K / Max: 70.0 K |
Specialist optics | Energy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV |
Details | LMB Krios1 |
Image recording | Image recording ID: 2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.7 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Electron microscopy #1~~
Microscopy ID | 1 |
---|---|
Microscope | FEI TITAN KRIOS |
Temperature | Min: 70.0 K / Max: 70.0 K |
Specialist optics | Energy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV |
Details | LMB Krios 2 |
Image recording | Image recording ID: 3 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.7 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing #1
+Image processing #2
+Image processing #3
+Image processing #4
-Atomic model buiding 1
Initial model |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
Details | Manual building was performed in Coot iterated with real space refinement in PHENIX. | ||||||||
Refinement | Space: REAL / Overall B value: 112 / Target criteria: Correlation coefficient | ||||||||
Output model | PDB-7ad3: |