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- EMDB-13880: Structure of the GPCR dimer Ste2 bound to an antagonist -

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Basic information

Entry
Database: EMDB / ID: EMD-13880
TitleStructure of the GPCR dimer Ste2 bound to an antagonist
Map data
Sample
  • Complex: GPCR dimer Ste2 bound to an antagonist
    • Protein or peptide: Pheromone alpha factor receptor
    • Protein or peptide: HIS-ALA-LEU-GLN-LEU-LYS-PRO-GLY-GLN-PRO-NLE-TYR
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: water
Function / homologymating-type factor pheromone receptor activity / GPCR fungal pheromone mating factor, STE2 / Pheromone alpha factor receptor, double transmembrane domain superfamily / Fungal pheromone mating factor STE2 GPCR / response to pheromone / membrane / Pheromone alpha factor receptor
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsVelazhahan V / Tate CG
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MRC U105197215 United Kingdom
CitationJournal: 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
DepositionNov 16, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateApr 6, 2022-
Current statusApr 6, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7qa8
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13880.png

Downloads & links

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Map

FileDownload / File: emd_13880.map.gz / Format: CCP4 / Size: 56.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 246 pix.
= 211.56 Å		0.86 Å/pix.
x 246 pix.
= 211.56 Å		0.86 Å/pix.
x 246 pix.
= 211.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0233 / Movie #1: 0.035
Minimum - Maximum-0.143397 - 0.21315639
Average (Standard dev.)0.00018421875 (±0.004805269)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions246246246
Spacing246246246
CellA=B=C: 211.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z246246246
origin x/y/z0.0000.0000.000
length x/y/z211.560211.560211.560
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS246246246
D min/max/mean-0.1430.2130.000

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Supplemental data

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Half map: #2

Fileemd_13880_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13880_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GPCR dimer Ste2 bound to an antagonist

EntireName: GPCR dimer Ste2 bound to an antagonist
Components
  • Complex: GPCR dimer Ste2 bound to an antagonist
    • Protein or peptide: Pheromone alpha factor receptor
    • Protein or peptide: HIS-ALA-LEU-GLN-LEU-LYS-PRO-GLY-GLN-PRO-NLE-TYR
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: water

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Supramolecule #1: GPCR dimer Ste2 bound to an antagonist

SupramoleculeName: GPCR dimer Ste2 bound to an antagonist / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Macromolecule #1: Pheromone alpha factor receptor

MacromoleculeName: Pheromone alpha factor receptor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 47.885402 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSDAAPSLSN LFYDPTYNPG QSTINYTSIY GNGSTITFDE LQGLVNSTVT QAIMFGVRCG AAALTLIVMW MTSRSRKTPI FIINQVSLF LIILHSALYF KYLLSNYSSV TYALTGFPQF ISRGDVHVYG ATNIIQVLLV ASIETSLVFQ IKVIFTGDNF K RIGLMLTS ...String:
MSDAAPSLSN LFYDPTYNPG QSTINYTSIY GNGSTITFDE LQGLVNSTVT QAIMFGVRCG AAALTLIVMW MTSRSRKTPI FIINQVSLF LIILHSALYF KYLLSNYSSV TYALTGFPQF ISRGDVHVYG ATNIIQVLLV ASIETSLVFQ IKVIFTGDNF K RIGLMLTS ISFTLGIATV TMYFVSAVKG MIVTYNDVSA TQDKYFNAST ILLASSINFM SFVLVVKLIL AIRSRRFLGL KQ FDSFHIL LIMSCQSLLV PSIIFILAYS LKPNQGTDVL TTVATLLAVL SLPLSSMWAT AANNASKTNT ITSDFTTSTD RFY PGTLSS FQTDSINNDA KSSLRSRLYD LYPRRKETTS DKHSERTFVS ETADDIEKNQ FYQLPTPTSS KNTRIGPFAD ASYK EGEVE PVDMYTPDTA ADEEARKFWT EDNNNL

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Macromolecule #2: HIS-ALA-LEU-GLN-LEU-LYS-PRO-GLY-GLN-PRO-NLE-TYR

MacromoleculeName: HIS-ALA-LEU-GLN-LEU-LYS-PRO-GLY-GLN-PRO-NLE-TYR / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.366606 KDa
SequenceString:
HALQLKPGQP (NLE)Y

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #4: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 4 / Number of copies: 34 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 70 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
In silico model: An ab initio 3D model was generated using the stochastic gradient descent algorithm implemented in RELION3.1
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136877
FSC plot (resolution estimation)

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