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- EMDB-33586: Cryo-EM structure of the octreotide-bound SSTR2-miniGq-scFv16 complex -

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Entry
Database: EMDB / ID: EMD-33586
TitleCryo-EM structure of the octreotide-bound SSTR2-miniGq-scFv16 complex
Map data
Sample
  • Complex: Complex of SSTR2-miniGq-scFv16 bound with octreotide
    • 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
    • Complex: G(q) subunit alpha, SSTR2, svFv16
      • Protein or peptide: Engineered Guanine nucleotide-binding protein G(q) subunit alpha
      • Protein or peptide: single Fab chain (svFv16)
      • Protein or peptide: Somatostatin receptor type 2
    • Complex: Octreotide
      • Protein or peptide: Octreotide
KeywordsGPCR / G protein / biased ligand / STRUCTURAL PROTEIN
Function / homology
Function and homology information


somatostatin receptor activity / peristalsis / neuropeptide binding / cellular response to glucocorticoid stimulus / response to starvation / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / neuropeptide signaling pathway / forebrain development / cerebellum development / Peptide ligand-binding receptors ...somatostatin receptor activity / peristalsis / neuropeptide binding / cellular response to glucocorticoid stimulus / response to starvation / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / neuropeptide signaling pathway / forebrain development / cerebellum development / Peptide ligand-binding receptors / PDZ domain binding / cellular response to estradiol stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / 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-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 / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / 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 / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / Ca2+ pathway / retina development in camera-type eye / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / fibroblast proliferation / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / spermatogenesis / G alpha (q) signalling events / Ras protein signal transduction / Extra-nuclear estrogen signaling / cell population proliferation / neuron projection / G protein-coupled receptor signaling pathway / lysosomal membrane / negative regulation of cell population proliferation / GTPase activity / synapse / protein-containing complex binding / signal transduction / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Somatostatin receptor 2 / Somatostatin receptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / 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 ...Somatostatin receptor 2 / Somatostatin receptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / 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. / WD domain, G-beta repeat / 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
Similarity search - Domain/homology
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: 3.3 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-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33586.png

Downloads & links

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Map

FileDownload / File: emd_33586.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 200 pix.
= 172. Å		0.86 Å/pix.
x 200 pix.
= 172. Å		0.86 Å/pix.
x 200 pix.
= 172. Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.48
Minimum - Maximum-2.6035109 - 4.5191774
Average (Standard dev.)0.0072848955 (±0.15433474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 172.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33586_half_map_1.map
Projections & Slices
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Density Histograms

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Half map: #1

Fileemd_33586_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex of SSTR2-miniGq-scFv16 bound with octreotide

EntireName: Complex of SSTR2-miniGq-scFv16 bound with octreotide
Components
  • Complex: Complex of SSTR2-miniGq-scFv16 bound with octreotide
    • 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
    • Complex: G(q) subunit alpha, SSTR2, svFv16
      • Protein or peptide: Engineered Guanine nucleotide-binding protein G(q) subunit alpha
      • Protein or peptide: single Fab chain (svFv16)
      • Protein or peptide: Somatostatin receptor type 2
    • Complex: Octreotide
      • Protein or peptide: Octreotide

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Supramolecule #1: Complex of SSTR2-miniGq-scFv16 bound with octreotide

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

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Supramolecule #2: 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: 2 / Parent: 1 / Macromolecule list: #1, #6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: G(q) subunit alpha, SSTR2, svFv16

SupramoleculeName: G(q) subunit alpha, SSTR2, svFv16 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2, #4-#5

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Supramolecule #4: Octreotide

SupramoleculeName: Octreotide / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: 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: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.198656 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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

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

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Macromolecule #2: Engineered Guanine nucleotide-binding protein G(q) subunit alpha

MacromoleculeName: Engineered Guanine nucleotide-binding protein G(q) subunit alpha
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.809506 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TVSAEDKAAA ERSKMIDKNL REDGEKARRT LRLLLLGADN SGKSTIVKQM RILHGGSGGS GGTSGIFETK FQVDKVNFHM FDVGGQRDE RRKWIQCFND VTAIIFVVDS SDYNRLQEAL NDFKSIWNNR WLRTISVILF LNKQDLLAEK VLAGKSKIED Y FPEFARYT ...String:
TVSAEDKAAA ERSKMIDKNL REDGEKARRT LRLLLLGADN SGKSTIVKQM RILHGGSGGS GGTSGIFETK FQVDKVNFHM FDVGGQRDE RRKWIQCFND VTAIIFVVDS SDYNRLQEAL NDFKSIWNNR WLRTISVILF LNKQDLLAEK VLAGKSKIED Y FPEFARYT TPEDATPEPG EDPRVTRAKY FIRKEFVDIS TASGDGRHIC YPHFTCAVDT ENARRIFNDC KDIILQMNLR EY NLV

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Macromolecule #3: Octreotide

MacromoleculeName: Octreotide / type: protein_or_peptide / ID: 3 / 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 #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: 27.713861 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VQLVESGGGL VQPGGSRKLS CSASGFAFSS FGMHWVRQAP EKGLEWVAYI SSGSGTIYYA DTVKGRFTIS RDDPKNTLFL QMTSLRSED TAMYYCVRSI YYYGSSPFDF WGQGTTLTVS SGGGSGGGGS GGGGSSDIVM TQATSSVPVT PGESVSISCR S SKSLLHSN ...String:
VQLVESGGGL VQPGGSRKLS CSASGFAFSS FGMHWVRQAP EKGLEWVAYI SSGSGTIYYA DTVKGRFTIS RDDPKNTLFL QMTSLRSED TAMYYCVRSI YYYGSSPFDF WGQGTTLTVS SGGGSGGGGS GGGGSSDIVM TQATSSVPVT PGESVSISCR S SKSLLHSN GNTYLYWFLQ RPGQSPQLLI YRMSNLASGV PERFSGSGSG TAFTLTISRL EAEDVGVYYC MQHLEYPLTF GA GTKLELK AAAHHHHHHH H

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Macromolecule #5: Somatostatin receptor type 2

MacromoleculeName: Somatostatin receptor type 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.759766 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 LCLVKVSGTD D

UniProtKB: Somatostatin receptor type 2

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Macromolecule #6: 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: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.845078 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFSAI L

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

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 608786
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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