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- EMDB-33231: Cryo-EM structure of the spexin-bound GALR2-miniGq complex -

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Basic information

Entry
Database: EMDB / ID: EMD-33231
TitleCryo-EM structure of the spexin-bound GALR2-miniGq complex
Map data
Sample
  • Complex: Spexin-bound Galanin receptor 2 in complex with Galphaq, Gbeta/gamma subunit and single chain variable fragment (scFv16)
    • Protein or peptide: spexin
    • Protein or peptide: Guanine nucleotide-binding protein G(q) subunit alpha
    • 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-chain variable fragment (scFv16)
    • Protein or peptide: Galanin receptor type 2
Function / homology
Function and homology information


galanin-activated signaling pathway / galanin receptor activity / positive regulation of large conductance calcium-activated potassium channel activity / inositol phosphate metabolic process / phosphatidylinositol metabolic process / feeding behavior / neuropeptide binding / peptide hormone binding / neuropeptide signaling pathway / muscle contraction ...galanin-activated signaling pathway / galanin receptor activity / positive regulation of large conductance calcium-activated potassium channel activity / inositol phosphate metabolic process / phosphatidylinositol metabolic process / feeding behavior / neuropeptide binding / peptide hormone binding / neuropeptide signaling pathway / muscle contraction / Peptide ligand-binding receptors / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / cilium / 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 / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / 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 / neuron projection development / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / 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 / positive regulation of cytosolic calcium ion concentration / 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 / learning or memory / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Galanin receptor 2 / Galanin 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 ...Galanin receptor 2 / Galanin 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. / 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
Similarity search - Domain/homology
Galanin 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: 3.5 Å
AuthorsJiang W / Zheng S
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structural insights into galanin receptor signaling.
Authors: Wentong Jiang / Sanduo Zheng /
Abstract: Galanin is a biologically active neuropeptide, and functions through three distinct G protein–coupled receptors (GPCRs), namely GALR1, GALR2, and GALR3. GALR signaling plays important roles in ...Galanin is a biologically active neuropeptide, and functions through three distinct G protein–coupled receptors (GPCRs), namely GALR1, GALR2, and GALR3. GALR signaling plays important roles in regulating various physiological processes such as energy metabolism, neuropathic pain, epileptic activity, and sleep homeostasis. GALR1 and GALR3 signal through the Gi/o pathway, whereas GALR2 signals mainly through the Gq/11 pathway. However, the molecular basis for galanin recognition and G protein selectivity of GALRs remains poorly understood. Here, we report the cryoelectron microscopy structures of the GALR1-Go and the GALR2-Gq complexes bound to the endogenous ligand galanin or spexin. The galanin peptide mainly adopts an alpha helical structure, which binds at the extracellular vestibule of the receptors, nearly parallel to the membrane plane without penetrating deeply into the receptor core. Structural analysis combined with functional studies reveals important structural determinants for the G protein selectivity of GALRs as well as other class A GPCRs. In addition, we show that the zinc ion is a negative allosteric regulator of GALR1 but not GALR2. Our studies provide insight into the mechanisms of G protein selectivity of GPCRs and highlight a potential function of the neuromodulator zinc ion as a modulator of GPCR signaling in the central nervous system.
History
DepositionApr 18, 2022-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateJun 29, 2022-
Current statusJun 29, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33231.png

Downloads & links

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Map

FileDownload / File: emd_33231.map.gz / Format: CCP4 / Size: 22.2 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.)
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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.465
Minimum - Maximum-1.8647587 - 2.7009249
Average (Standard dev.)-0.00055859715 (±0.08973989)
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: #1

Fileemd_33231_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_33231_half_map_2.map
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Sample components

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Entire : Spexin-bound Galanin receptor 2 in complex with Galphaq, Gbeta/ga...

EntireName: Spexin-bound Galanin receptor 2 in complex with Galphaq, Gbeta/gamma subunit and single chain variable fragment (scFv16)
Components
  • Complex: Spexin-bound Galanin receptor 2 in complex with Galphaq, Gbeta/gamma subunit and single chain variable fragment (scFv16)
    • Protein or peptide: spexin
    • Protein or peptide: Guanine nucleotide-binding protein G(q) subunit alpha
    • 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-chain variable fragment (scFv16)
    • Protein or peptide: Galanin receptor type 2

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Supramolecule #1: Spexin-bound Galanin receptor 2 in complex with Galphaq, Gbeta/ga...

SupramoleculeName: Spexin-bound Galanin receptor 2 in complex with Galphaq, Gbeta/gamma subunit and single chain variable fragment (scFv16)
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens, synthetic construct

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Macromolecule #1: spexin

MacromoleculeName: spexin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.621876 KDa
Recombinant expressionOrganism: synthetic construct (others)
SequenceString:
NWTPQAMLYL KGAQ

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

MacromoleculeName: 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: 28.180963 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPMGSTVSAE DKAAAERSKM IDKNLREDGE KARRTLRLLL LGADNSGKST IVKQMRILHG GSGGSGGTSG IFETKFQVDK VNFHMFDVG GQRDERRKWI QCFNDVTAII FVVDSSDYNR LQEALNDFKS IWNNRWLRTI SVILFLNKQD LLAEKVLAGK S KIEDYFPE ...String:
GPMGSTVSAE DKAAAERSKM IDKNLREDGE KARRTLRLLL LGADNSGKST IVKQMRILHG GSGGSGGTSG IFETKFQVDK VNFHMFDVG GQRDERRKWI QCFNDVTAII FVVDSSDYNR LQEALNDFKS IWNNRWLRTI SVILFLNKQD LLAEKVLAGK S KIEDYFPE FARYTTPEAA TPEPGDDPRV TRAKYFIRKE FVDISTASGD GRHICYPHFT CAVDTENARR IFNDCKDIIL QM NLREYNL V

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Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.389934 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HHHHHHGSMS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLVS ASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG HTGYLSCCRF L DDNQIVTS ...String:
HHHHHHGSMS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLVS ASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG HTGYLSCCRF L DDNQIVTS SGDTTCALWD IETGQQTTTF TGHTGDVMSL SLAPDTRLFV SGACDASAKL WDVREGMCRQ TFTGHESDIN AI CFFPNGN AFATGSDDAT CRLFDLRADQ ELMTYSHDNI ICGITSVSFS KSGRLLLAGY DDFNCNVWDA LKADRAGVLA GHD NRVSCL GVTDDGMAVA TGSWDSFLKI WN

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Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.845078 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFSAI L

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Macromolecule #5: single-chain variable fragment (scFv16)

MacromoleculeName: single-chain variable fragment (scFv16) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.071615 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GRPDVQLVES GGGLVQPGGS RKLSCSASGF AFSSFGMHWV RQAPEKGLEW VAYISSGSGT IYYADTVKGR FTISRDDPKN TLFLQMTSL RSEDTAMYYC VRSIYYYGSS PFDFWGQGTT LTVSSGGGGS GGGGSGGGGS DIVMTQATSS VPVTPGESVS I SCRSSKSL ...String:
GRPDVQLVES GGGLVQPGGS RKLSCSASGF AFSSFGMHWV RQAPEKGLEW VAYISSGSGT IYYADTVKGR FTISRDDPKN TLFLQMTSL RSEDTAMYYC VRSIYYYGSS PFDFWGQGTT LTVSSGGGGS GGGGSGGGGS DIVMTQATSS VPVTPGESVS I SCRSSKSL LHSNGNTYLY WFLQRPGQSP QLLIYRMSNL ASGVPDRFSG SGSGTAFTLT ISRLEAEDVG VYYCMQHLEY PL TFGAGTK LELKAAAGAP LEVLFQGPGA WSHPQFEKGA EDQVDPRLID GKGAAHHHHH HHH

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Macromolecule #6: Galanin receptor type 2

MacromoleculeName: Galanin receptor type 2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.401867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKGS MNVSGCPGAG NASQAGGGGG WHPEAVIVPL LFALIFLVGT VGNTLVLAVL LRGGQAVSTT NLFILNLGVA DLCFILCCV PFQATIYTLD GWVFGSLLCK AVHFLIFLTM HASSFTLAAV SLDRYLAIRY PLHSRELRTP RNALAAIGLI W GLSLLFSG ...String:
DYKDDDDKGS MNVSGCPGAG NASQAGGGGG WHPEAVIVPL LFALIFLVGT VGNTLVLAVL LRGGQAVSTT NLFILNLGVA DLCFILCCV PFQATIYTLD GWVFGSLLCK AVHFLIFLTM HASSFTLAAV SLDRYLAIRY PLHSRELRTP RNALAAIGLI W GLSLLFSG PYLSYYQQSQ LANLTVCHPA WSAPRRRAMD ICTFVFSYLL PVLVLGLTYA RTLRYLWRAV DPVAAGSGAR RA KRKVTRM ILIVAALFCL CWMPHHALIL CVWFGQFPLT RATYALRILS HLVSYANSCV NPIVYALVSK HFRKGFRTIC AGL LGRAGS LEVLFQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration5.6 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
25.0 mMHEPEs
150.0 nMNaCl
0.01 g/100mlLMNG
100.0 nMgalanin
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.3000000000000003 µm / Nominal defocus min: 1.2 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 332603
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7xjl:
Cryo-EM structure of the spexin-bound GALR2-miniGq complex

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