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- EMDB-11720: Class D GPCR Ste2 dimer coupled to two G proteins -

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Basic information

Entry
Database: EMDB / ID: EMD-11720
TitleClass D GPCR Ste2 dimer coupled to two G proteins
Map dataMap1
Sample
  • Complex: Ste2 dimer coupled to two G proteins
    • Complex: Ste2 dimer coupled to two G proteins
      • Protein or peptide: Pheromone alpha factor receptor
      • Protein or peptide: STE4 isoform 1
      • Protein or peptide: Guanine nucleotide-binding protein subunit gamma
    • Complex: Alpha-factor mating pheromone
      • Protein or peptide: Alpha-factor mating pheromone
    • Complex: Guanine nucleotide-binding protein alpha-1 subunit,Guanine nucleotide-binding protein alpha-1 subunit
      • Protein or peptide: Guanine nucleotide-binding protein alpha-1 subunit,Guanine nucleotide-binding protein alpha-1 subunit
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsFungal GPCR / Dimer / Complex / Class D / Active State / MEMBRANE PROTEIN
Function / homology
Function and homology information


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 / G-protein beta/gamma-subunit complex / regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion ...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 / G-protein beta/gamma-subunit complex / regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion / chemotropism / Cdc24p-Far1p-Gbetagamma complex / G alpha (12/13) signalling events / CDC42 GTPase cycle / mating pheromone activity / mating-type factor pheromone receptor activity / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / nuclear migration involved in conjugation with cellular fusion / mating / G protein-coupled receptor homodimeric complex / response to pheromone triggering conjugation with cellular fusion / karyogamy involved in conjugation with cellular fusion / regulation of carbohydrate metabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / 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 / cupric ion binding / G-protein alpha-subunit binding / cell periphery / G protein-coupled receptor binding / small GTPase binding / G-protein beta/gamma-subunit complex binding / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / scaffold protein binding / cell cortex / endosome / endosome membrane / G protein-coupled receptor signaling pathway / GTPase activity / protein kinase binding / GTP binding / signal transduction / extracellular region / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Fungal G-protein, alpha subunit / Guanine nucleotide-binding protein subunit gamma, fungal / Mating factor alpha, C-terminal repeat / Mating factor alpha precursor, N-terminal / Yeast mating factor alpha hormone / Mating factor alpha precursor N-terminus / GPCR fungal pheromone mating factor, STE2 / : / Pheromone alpha factor receptor, double transmembrane domain superfamily / Fungal pheromone mating factor STE2 GPCR ...Fungal G-protein, alpha subunit / Guanine nucleotide-binding protein subunit gamma, fungal / Mating factor alpha, C-terminal repeat / Mating factor alpha precursor, N-terminal / Yeast mating factor alpha hormone / Mating factor alpha precursor N-terminus / GPCR fungal pheromone mating factor, STE2 / : / Pheromone alpha factor receptor, double transmembrane domain superfamily / Fungal pheromone mating factor STE2 GPCR / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein subunit gamma / BJ4_G0036910.mRNA.1.CDS.1 / Mating factor alpha-1 / Guanine nucleotide-binding protein alpha-1 subunit / Pheromone alpha factor receptor / Guanine nucleotide-binding protein subunit beta / Guanine nucleotide-binding protein subunit gamma
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsVelazhahan V / Tate C
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MRC U105197215 United Kingdom
European Research Council (ERC)EMPSI 339995 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
DepositionSep 14, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing 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
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  • 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-7ad3
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11720.png

Downloads & links

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Map

FileDownload / File: emd_11720.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 210 pix.
= 219.87 Å		1.05 Å/pix.
x 210 pix.
= 219.87 Å		1.05 Å/pix.
x 210 pix.
= 219.87 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.035
Minimum - Maximum-0.18854322 - 0.23770761
Average (Standard dev.)0.00028280867 (±0.005858397)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 219.87001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0471.0471.047
M x/y/z210210210
origin x/y/z0.0000.0000.000
length x/y/z219.870219.870219.870
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS210210210
D min/max/mean-0.1890.2380.000

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Supplemental data

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Additional map: Map2

Fileemd_11720_additional_1.map
AnnotationMap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap1 for calculating map1

Fileemd_11720_half_map_1.map
AnnotationHalfmap1 for calculating map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap2 for calculating map1

Fileemd_11720_half_map_2.map
AnnotationHalfmap2 for calculating map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ste2 dimer coupled to two G proteins

EntireName: Ste2 dimer coupled to two G proteins
Components
  • Complex: Ste2 dimer coupled to two G proteins
    • Complex: Ste2 dimer coupled to two G proteins
      • Protein or peptide: Pheromone alpha factor receptor
      • Protein or peptide: STE4 isoform 1
      • Protein or peptide: Guanine nucleotide-binding protein subunit gamma
    • Complex: Alpha-factor mating pheromone
      • Protein or peptide: Alpha-factor mating pheromone
    • Complex: Guanine nucleotide-binding protein alpha-1 subunit,Guanine nucleotide-binding protein alpha-1 subunit
      • Protein or peptide: Guanine nucleotide-binding protein alpha-1 subunit,Guanine nucleotide-binding protein alpha-1 subunit
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: Ste2 dimer coupled to two G proteins

SupramoleculeName: Ste2 dimer coupled to two G proteins / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Molecular weightTheoretical: 266.7 KDa

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Supramolecule #2: Ste2 dimer coupled to two G proteins

SupramoleculeName: Ste2 dimer coupled to two G proteins / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3, #5
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: Alpha-factor mating pheromone

SupramoleculeName: Alpha-factor mating pheromone / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #4: Guanine nucleotide-binding protein alpha-1 subunit,Guanine nucleo...

SupramoleculeName: Guanine nucleotide-binding protein alpha-1 subunit,Guanine nucleotide-binding protein alpha-1 subunit
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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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

UniProtKB: Pheromone alpha factor receptor

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Macromolecule #2: Alpha-factor mating pheromone

MacromoleculeName: Alpha-factor mating pheromone / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.685986 KDa
SequenceString:
WHWLQLKPGQ PMY

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Macromolecule #3: STE4 isoform 1

MacromoleculeName: STE4 isoform 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 46.626953 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAAHQMDSIT YSNNVTQQYI QPQSLQDISA VEDEIQNKIE AARQESKQLH AQINKAKHKI QDASLFQMAN KVTSLTKNKI NLKPNIVLK GHNNKISDFR WSRDSKRILS ASQDGFMLIW DSASGLKQNA IPLDSQWVLS CAISPSSTLV ASAGLNNNCT I YRVSKENR ...String:
MAAHQMDSIT YSNNVTQQYI QPQSLQDISA VEDEIQNKIE AARQESKQLH AQINKAKHKI QDASLFQMAN KVTSLTKNKI NLKPNIVLK GHNNKISDFR WSRDSKRILS ASQDGFMLIW DSASGLKQNA IPLDSQWVLS CAISPSSTLV ASAGLNNNCT I YRVSKENR VAQNVASIFK GHTCYISDIE FTDNAHILTA SGDMTCALWD IPKAKRVREY SDHLGDVLAL AIPEEPNSEN SS NTFASCG SDGYTYIWDS RSPSAVQSFY VNDSDINALR FFKDGMSIVA GSDNGAINMY DLRSDCSIAT FSLFRGYEER TPT PTYMAA NMEYNTAQSP QTLKSTSSSY LDNQGVVSLD FSASGRLMYS CYTDIGCVVW DVLKGEIVGK LEGHGGRVTG VRSS PDGLA VCTGSWDSTM KIWSPGYQ

UniProtKB: BJ4_G0036910.mRNA.1.CDS.1

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Macromolecule #4: Guanine nucleotide-binding protein alpha-1 subunit,Guanine nucleo...

MacromoleculeName: Guanine nucleotide-binding protein alpha-1 subunit,Guanine nucleotide-binding protein alpha-1 subunit
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 26.316305 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: TVSTQTIGDE SDPFLQNKRA NDVIEQSLQL EKQRDKNEIK LLLLGADNSG KSTVLKQLKL LHGGSGGSGG TTGITETEFN IGSSKFKVL DAGGQRSERK KWIHCFEGIT AVLFVLDMSD YNRMHESIML FDTLLNSKWF KDTPFILFLN KIDLFEEKVK S MPIRKYFP ...String:
TVSTQTIGDE SDPFLQNKRA NDVIEQSLQL EKQRDKNEIK LLLLGADNSG KSTVLKQLKL LHGGSGGSGG TTGITETEFN IGSSKFKVL DAGGQRSERK KWIHCFEGIT AVLFVLDMSD YNRMHESIML FDTLLNSKWF KDTPFILFLN KIDLFEEKVK S MPIRKYFP DYQGRVGDAE AGLKYFEKIF LSLNKTNKPI YVKRTCATDT QTAKFILSAV TDLIIQQNLK KIGII

UniProtKB: Guanine nucleotide-binding protein alpha-1 subunit, Guanine nucleotide-binding protein alpha-1 subunit

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Macromolecule #5: Guanine nucleotide-binding protein subunit gamma

MacromoleculeName: Guanine nucleotide-binding protein subunit gamma / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 12.477051 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
TSVQNSPRLQ QPQEQQQQQQ QLSLKIKQLK LKRINELNNK LRKELSRERI TASNACLTII NYTSNTKDYT LPELWGYPVA GSNHFIEGL KNAQKNSQMS NSNSVSSTLM

UniProtKB: Guanine nucleotide-binding protein subunit gamma

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 7 / Number of copies: 6 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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

Concentration0.7 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
100.0 mMNaClSodium Chloride
2.0 mMMgCl2Magnesium Chloride
0.001 %LMNGLauryl Maltose Neopentyl Glycol
0.001 mMWHWLQLKPGQPMYAlpha-factor

Details: Solutions were made fresh and filtered
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was purified as a monodisperse complex

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV
DetailseBIC Krios1
Image recordingImage recording ID: 1 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV
DetailsLMB Krios1
Image recordingImage recording ID: 2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~~

Microscopy ID1
MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV
DetailsLMB Krios 2
Image recordingImage recording ID: 3 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Image recording ID1
Particle selectionNumber selected: 2193519
Startup modelType of model: INSILICO MODEL
Details: Ab inito model generated by stochastic gradient descent implemented within RELION-3.1
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 96611
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Image processing #2

Image processing ID2
Image recording ID2
Particle selectionNumber selected: 485568
Startup modelType of model: INSILICO MODEL
In silico model: Ab inito model generated by stochastic gradient descent implemented within RELION-3.1
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1)
Details: 16418 particles from this dataset contributed to the final 131274 particles that provided map 2 at 3.3 angstrom global resolution
Number images used: 16418
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Image processing #3

Image processing ID3
Image recording ID3
Particle selectionNumber selected: 781447
Startup modelType of model: INSILICO MODEL
In silico model: Ab inito model generated by stochastic gradient descent implemented within RELION-3.1
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION
Details: 4556 particles from this dataset contributed to the final 131274 particles that provided map 2 at 3.3 angstrom global resolution
Number images used: 4556
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Image processing #4

Image processing ID4
Image recording ID1
Particle selectionNumber selected: 2193519
Startup modelType of model: INSILICO MODEL
In silico model: Ab inito model generated by stochastic gradient descent implemented within RELION-3.1
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
Details: 110300 particles from this dataset contributed to the final 131274 particles that provided map 2 at 3.3 angstrom global resolution
Number images used: 110300
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6g79

chain_id: A, source_name: PDB, initial_model_type: experimental model

6g79

chain_id: B, source_name: PDB, initial_model_type: experimental model

6g79

chain_id: G, source_name: PDB, initial_model_type: experimental model
DetailsManual building was performed in Coot iterated with real space refinement in PHENIX.
RefinementSpace: REAL / Overall B value: 112 / Target criteria: Correlation coefficient
Output model

PDB-7ad3:
Class D GPCR Ste2 dimer coupled to two G proteins

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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