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- EMDB-33585: Cryo-EM structure of the octreotide-bound SSTR2-miniGo-scFv16 complex -

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Entry
Database: EMDB / ID: EMD-33585
TitleCryo-EM structure of the octreotide-bound SSTR2-miniGo-scFv16 complex
Map data
Sample
  • Complex: complex of SSTR2-miniGo-scFv16 bound with octreotide
    • Complex: G(o) subunit alpha
      • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha
    • Complex: G(I)/G(S)/G(T) subunit beta-1, G(I)/G(S)/G(O) subunit gamma-2
      • 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: single Fab chain (svFv16)
    • Complex: svFv16, octreotide
      • Protein or peptide: Octreotide
    • Complex: Somatostatin receptor type 2
      • Protein or peptide: Somatostatin receptor type 2
Function / homology
Function and homology information


somatostatin receptor activity / peristalsis / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / vesicle docking involved in exocytosis / neuropeptide binding / cellular response to glucocorticoid stimulus / G protein-coupled dopamine receptor signaling pathway / regulation of heart contraction / response to starvation ...somatostatin receptor activity / peristalsis / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / vesicle docking involved in exocytosis / neuropeptide binding / cellular response to glucocorticoid stimulus / G protein-coupled dopamine receptor signaling pathway / regulation of heart contraction / response to starvation / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / neuropeptide signaling pathway / negative regulation of insulin secretion / G protein-coupled serotonin receptor binding / forebrain development / muscle contraction / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cerebellum development / Peptide ligand-binding receptors / cellular response to estradiol stimulus / locomotory behavior / PDZ domain binding / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / adenylate cyclase-modulating G protein-coupled receptor 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-coupled acetylcholine receptor signaling pathway / G-protein activation / 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 / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / cellular response to prostaglandin E stimulus / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / cell body / G alpha (i) signalling events / fibroblast proliferation / spermatogenesis / G alpha (s) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / neuron projection / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / lysosomal membrane / GTPase activity / dendrite / synapse / protein-containing complex binding / GTP binding / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Somatostatin receptor 2 / Somatostatin receptor family / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / 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 subunit ...Somatostatin receptor 2 / Somatostatin receptor family / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / 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 subunit / G-protein gamma subunit domain profile. / 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 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 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. / WD domain, G-beta repeat / 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 G(o) subunit alpha / Somatostatin receptor type 2 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsChen S / Zheng S
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Nat Chem Biol / Year: 2023
Title: Molecular basis for the selective G protein signaling of somatostatin receptors.
Authors: Sijia Chen / Xiao Teng / Sanduo Zheng /
Abstract: G protein-coupled receptors (GPCRs) modulate every aspect of physiological functions mainly through activating heterotrimeric G proteins. A majority of GPCRs promiscuously couple to multiple G ...G protein-coupled receptors (GPCRs) modulate every aspect of physiological functions mainly through activating heterotrimeric G proteins. A majority of GPCRs promiscuously couple to multiple G protein subtypes. Here we validate that in addition to the well-known G pathway, somatostatin receptor 2 and 5 (SSTR2 and SSTR5) couple to the G pathway and show that smaller ligands preferentially activate the G pathway. We further determined cryo-electron microscopy structures of the SSTR2‒G and SSTR2‒G complexes bound to octreotide and SST-14. Structural and functional analysis revealed that G protein selectivity of SSTRs is not only determined by structural elements in the receptor-G protein interface, but also by the conformation of the agonist-binding pocket. Accordingly, smaller ligands fail to stabilize a broader agonist-binding pocket of SSTRs that is required for efficient G coupling but not G coupling. Our studies facilitate the design of drugs with selective G protein signaling to improve therapeutic efficacy.
History
DepositionJun 9, 2022-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33585.png

Downloads & links

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Map

FileDownload / File: emd_33585.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 180 pix.
= 195.66 Å		1.09 Å/pix.
x 180 pix.
= 195.66 Å		1.09 Å/pix.
x 180 pix.
= 195.66 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.8006113 - 2.859596
Average (Standard dev.)-0.0009298809 (±0.075182855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 195.66 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33585_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33585_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : complex of SSTR2-miniGo-scFv16 bound with octreotide

EntireName: complex of SSTR2-miniGo-scFv16 bound with octreotide
Components
  • Complex: complex of SSTR2-miniGo-scFv16 bound with octreotide
    • Complex: G(o) subunit alpha
      • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha
    • Complex: G(I)/G(S)/G(T) subunit beta-1, G(I)/G(S)/G(O) subunit gamma-2
      • 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: single Fab chain (svFv16)
    • Complex: svFv16, octreotide
      • Protein or peptide: Octreotide
    • Complex: Somatostatin receptor type 2
      • Protein or peptide: Somatostatin receptor type 2

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Supramolecule #1: complex of SSTR2-miniGo-scFv16 bound with octreotide

SupramoleculeName: complex of SSTR2-miniGo-scFv16 bound with octreotide / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: G(o) subunit alpha

SupramoleculeName: G(o) subunit alpha / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: G(I)/G(S)/G(T) subunit beta-1, G(I)/G(S)/G(O) subunit gamma-2

SupramoleculeName: G(I)/G(S)/G(T) subunit beta-1, G(I)/G(S)/G(O) subunit gamma-2
type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2-#4

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Supramolecule #4: svFv16, octreotide

SupramoleculeName: svFv16, octreotide / type: complex / ID: 4 / Chimera: Yes / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: Somatostatin receptor type 2

SupramoleculeName: Somatostatin receptor type 2 / type: complex / ID: 5 / Chimera: Yes / Parent: 1 / Macromolecule list: #6

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Macromolecule #1: Guanine nucleotide-binding protein G(o) subunit alpha

MacromoleculeName: Guanine nucleotide-binding protein G(o) subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.056553 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LSAEERAALE RSKAIEKNLK EDGISAAKDV KLLLLGADNS GKSTIVKQMK IIHGGSGGSG GTTGIVETHF TFKNLHFRLF DVGGQRSER KKWIHCFEDV TAIIFCVDLS DYNRMHESLM DFDSICNNKF FIDTSIILFL NKKDLFGEKI KKSPLTICFP E YTGPNTYE ...String:
LSAEERAALE RSKAIEKNLK EDGISAAKDV KLLLLGADNS GKSTIVKQMK IIHGGSGGSG GTTGIVETHF TFKNLHFRLF DVGGQRSER KKWIHCFEDV TAIIFCVDLS DYNRMHESLM DFDSICNNKF FIDTSIILFL NKKDLFGEKI KKSPLTICFP E YTGPNTYE DAAAYIQAQF ESKNRSPNKE IYCHMTCATD TNNAQVIFDA VTDIIIANNL RGCGLY

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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: 37.198656 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLVS ASQDGKLIIW DSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG HTGYLSCCRF LDDNQIVTSS G DTTCALWD ...String:
ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLVS ASQDGKLIIW DSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG HTGYLSCCRF LDDNQIVTSS G DTTCALWD IETGQQTTTF TGHTGDVMSL SLAPDTRLFV SGACDASAKL WDVREGMCRQ TFTGHESDIN AICFFPNGNA FA TGSDDAT CRLFDLRADQ ELMTYSHDNI ICGITSVSFS KSGRLLLAGY DDFNCNVWDA LKADRAGVLA GHDNRVSCLG VTD DGMAVA 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: 6.160126 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
ASIAQARKLV EQLKMEANID RIKVSKAAAD LMAYCEAHAK EDPLLTPVPA SENPFR

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Macromolecule #4: single Fab chain (svFv16)

MacromoleculeName: single Fab chain (svFv16) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.222219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VQLVESGGGL VQPGGSRKLS CSASGFAFSS FGMHWVRQAP EKGLEWVAYI SSGSGTIYYA DTVKGRFTIS RDDPKNTLFL QMTSLRSED TAMYYCVRSI YYYGSSPFDF WGQGTTLTVS SGGGGSGGGG SGGGGSDIVM TQATSSVPVT PGESVSISCR S SKSLLHSN ...String:
VQLVESGGGL VQPGGSRKLS CSASGFAFSS FGMHWVRQAP EKGLEWVAYI SSGSGTIYYA DTVKGRFTIS RDDPKNTLFL QMTSLRSED TAMYYCVRSI YYYGSSPFDF WGQGTTLTVS SGGGGSGGGG SGGGGSDIVM TQATSSVPVT PGESVSISCR S SKSLLHSN GNTYLYWFLQ RPGQSPQLLI YRMSNLASGV PDRFSGSGSG TAFTLTISRL EAEDVGVYYC MQHLEYPLTF GA GTKLEL

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Macromolecule #5: Octreotide

MacromoleculeName: Octreotide / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.036246 KDa
SequenceString:
(DPN)CF(DTR)KTCT

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Macromolecule #6: Somatostatin receptor type 2

MacromoleculeName: Somatostatin receptor type 2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.740621 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDMADEPLNG SHTWLSIPFD LNGSVVSTNT SNQTEPYYDL TSNAVLTFIY FVVCIIGLCG NTLVIYVILR YAKMKTITNI YILNLAIAD ELFMLGLPFL AMQVALVHWP FGKAICRVVM TVDGINQFTS IFCLTVMSID RYLAVVHPIK SAKWRRPRTA K MITMAVWG ...String:
MDMADEPLNG SHTWLSIPFD LNGSVVSTNT SNQTEPYYDL TSNAVLTFIY FVVCIIGLCG NTLVIYVILR YAKMKTITNI YILNLAIAD ELFMLGLPFL AMQVALVHWP FGKAICRVVM TVDGINQFTS IFCLTVMSID RYLAVVHPIK SAKWRRPRTA K MITMAVWG VSLLVILPIM IYAGLRSNQW GRSSCTINWP GESGAWYTGF IIYTFILGFL VPLTIICLCY LFIIIKVKSS GI RVGSSKR KKSEKKVTRM VSIVVAVFIF CWLPFYIFNV SSVSMAISPT PALKGMFDFV VVLTYANSCA NPILYAFLSD NFK KSFQNV L

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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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 687989
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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