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- EMDB-29684: Cryo-EM structure of ADGRF1 coupled to miniGs/q -

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Basic information

Entry
Database: EMDB / ID: EMD-29684
TitleCryo-EM structure of ADGRF1 coupled to miniGs/q
Map data
Sample
  • Complex: Tethered agonist activated adhesion GPCR ADGRF1 coupled to miniGs/q
    • Protein or peptide: MiniG alpha s/q chimera
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Nanobody 35Single-domain antibody
    • Protein or peptide: Adhesion G-protein-coupled receptor F1
  • Ligand: [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE
Function / homology
Function and homology information


G protein-coupled receptor activity / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits ...G protein-coupled receptor activity / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / G-protein beta-subunit binding / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GPCR family 2, Ig-hepta-like receptor / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GPS domain profile. / G-protein-coupled receptor proteolytic site domain / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. ...GPCR family 2, Ig-hepta-like receptor / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GPS domain profile. / G-protein-coupled receptor proteolytic site domain / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Adhesion G protein-coupled receptor F1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsJones D / Rawson S / Blacklow S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R35 CA220340 United States
CitationJournal: Nat Commun / Year: 2023
Title: Tethered agonist activated ADGRF1 structure and signalling analysis reveal basis for G protein coupling.
Authors: Daniel T D Jones / Andrew N Dates / Shaun D Rawson / Maggie M Burruss / Colin H Lipper / Stephen C Blacklow /
Abstract: Adhesion G Protein Coupled Receptors (aGPCRs) have evolved an activation mechanism to translate extracellular force into liberation of a tethered agonist (TA) to effect cell signalling. We report ...Adhesion G Protein Coupled Receptors (aGPCRs) have evolved an activation mechanism to translate extracellular force into liberation of a tethered agonist (TA) to effect cell signalling. We report here that ADGRF1 can signal through all major G protein classes and identify the structural basis for a previously reported Gα preference by cryo-EM. Our structure shows that Gα preference in ADGRF1 may derive from tighter packing at the conserved F569 of the TA, altering contacts between TM helix I and VII, with a concurrent rearrangement of TM helix VII and helix VIII at the site of Gα recruitment. Mutational studies of the interface and of contact residues within the 7TM domain identify residues critical for signalling, and suggest that Gα signalling is more sensitive to mutation of TA or binding site residues than Gα. Our work advances the detailed molecular understanding of aGPCR TA activation, identifying features that potentially explain preferential signal modulation.
History
DepositionFeb 6, 2023-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateMay 10, 2023-
Current statusMay 10, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29684.png

Downloads & links

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Map

FileDownload / File: emd_29684.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.9918474 - 1.6080468
Average (Standard dev.)-0.0002484315 (±0.030965237)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #2

Fileemd_29684_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram (log scale)

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Additional map: #1

Fileemd_29684_additional_2.map
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Half map: #2

Fileemd_29684_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_29684_half_map_2.map
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Sample components

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Entire : Tethered agonist activated adhesion GPCR ADGRF1 coupled to miniGs/q

EntireName: Tethered agonist activated adhesion GPCR ADGRF1 coupled to miniGs/q
Components
  • Complex: Tethered agonist activated adhesion GPCR ADGRF1 coupled to miniGs/q
    • Protein or peptide: MiniG alpha s/q chimera
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Nanobody 35Single-domain antibody
    • Protein or peptide: Adhesion G-protein-coupled receptor F1
  • Ligand: [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE

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Supramolecule #1: Tethered agonist activated adhesion GPCR ADGRF1 coupled to miniGs/q

SupramoleculeName: Tethered agonist activated adhesion GPCR ADGRF1 coupled to miniGs/q
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: MiniG alpha s/q chimera

MacromoleculeName: MiniG alpha s/q chimera / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.835914 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVFTLEDFVG DWEQTAAYNL DQVLEQGGVS SLLQNLAVSV TPIQRIVRSG ENALKIDIHV IIPYEGLSAD QMAQIEEVFK VVYPVDDHH FKVILPYGTL VIDGVTPNML NYFGRPYEGI AVFDGKKITV TGTLWNGNKI IDERLITPDG SMLFRVTINS G GGGSGGGG ...String:
MVFTLEDFVG DWEQTAAYNL DQVLEQGGVS SLLQNLAVSV TPIQRIVRSG ENALKIDIHV IIPYEGLSAD QMAQIEEVFK VVYPVDDHH FKVILPYGTL VIDGVTPNML NYFGRPYEGI AVFDGKKITV TGTLWNGNKI IDERLITPDG SMLFRVTINS G GGGSGGGG SSGEFEFNSK TEDQRNEEKA QREANKKIEK QLQKDKQVYR ATHRLLLLGA DNSGKSTIVK QMRILHGGSG GS GGTSGIF ETKFQVDKVN FHMFDVGGQR DERRKWIQCF NDVTAIIFVV DSSDYNRLQE ALNLFKSIWN NRWLRTISVI LFL NKQDLL AEKVLAGKSK IEDYFPEFAR YTTPEDATPE PGEDPRVTRA KYFIRDEFLR ISTASGDGRH YCYPHFTCAV DTEN ARRIF NDCKDIILQM NLREYNLV

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.418086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHLEV LFQGPGSSGS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR ...String:
MHHHHHHLEV LFQGPGSSGS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR FLDDNQIVTS SGDTTCALWD IETGQQTTTF TGHTGDVMSL SLAPDTRLFV SGACDASAKL WDVREGMCRQ TF TGHESDI NAICFFPNGN AFATGSDDAT CRLFDLRADQ ELMTYSHDNI ICGITSVSFS KSGRLLLAGY DDFNCNVWDA LKA DRAGVL AGHDNRVSCL GVTDDGMAVA TGSWDSFLKI WN

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

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Macromolecule #4: Nanobody 35

MacromoleculeName: Nanobody 35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 19.726197 KDa
Recombinant expressionOrganism: Lama glama (llama)
SequenceString:
MKYLLPTAAA GLLLLAAQPA MAQVQLQESG GGLVQPGGSL RLSCAASGFT FSNYKMNWVR QAPGKGLEWV SDISQSGARI SYTGSVKGR FTISRDNAKN TLYLQMNSLK PEDTAVYYCA RCPAPFTRDC FDVTSTTYAY RGQGTQVTVS SLEVLFQGPG H HHHHHHHG SEDQVDPRLI DGK

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Macromolecule #5: Adhesion G-protein-coupled receptor F1

MacromoleculeName: Adhesion G-protein-coupled receptor F1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.837516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSYI FCLVFADYKD HDGDYKDHDI DYKDDDDKEN LYFQTSFSIL MSPFVPSTIF PVVKWITYVG LGISIGSLIL CLIIEALFW KQIKKSQTSH TRRICMVNIA LSLLIADVWF IVGATVDTTV NPSGVCTAAV FFTHFFYLSL FFWMLMLGIL L AYRIILVF ...String:
MKTIIALSYI FCLVFADYKD HDGDYKDHDI DYKDDDDKEN LYFQTSFSIL MSPFVPSTIF PVVKWITYVG LGISIGSLIL CLIIEALFW KQIKKSQTSH TRRICMVNIA LSLLIADVWF IVGATVDTTV NPSGVCTAAV FFTHFFYLSL FFWMLMLGIL L AYRIILVF HHMAQHLMMA VGFCLGYGCP LIISVITIAV TQPSNTYKRK DVCWLNWSNG SKPLLAFVVP ALAIVAVNFV VV LLVLTKL WRPTVGERLS RDDKATIIRV GKSLLILTPL LGLTWGFGIG TIVDSQNLAW HVIFALLNAF QGFFILCFGI LLD SKLRQL LFNKLSALSS WKQTEKQNSS DLSAKPKFSK PFNPLQNKGH YAFSHTGDSS DNIMLTQFVS NEGGGGSGGG GSSG VTGYR LFEEIL

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Macromolecule #6: [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE

MacromoleculeName: [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: LPC
Molecular weightTheoretical: 468.585 Da
Chemical component information

ChemComp-LPC:
[1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE

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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

Concentration8 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7wu3

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73903
FSC plot (resolution estimation)

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