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- EMDB-39365: Cryo-EM structure of ADGRG2-Gs complex with NTF nanobody -

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Entry
Database: EMDB / ID: EMD-39365
TitleCryo-EM structure of ADGRG2-Gs complex with NTF nanobody
Map data
Sample
  • Complex: Complex of ADGRG2 with nanonody and G protein trimer
    • Protein or peptide: Guanine nucleotide-binding protein G(s) 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 subunit gamma
    • Protein or peptide: Nanobody-35
    • Protein or peptide: Adhesion G-protein coupled receptor G2
    • Protein or peptide: ScFv-16
  • Ligand: 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE
KeywordsGPCR / MEMBRANE PROTEIN
Function / homology
Function and homology information


Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / sensory perception of chemical stimulus / Activation of the phototransduction cascade / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / beta-2 adrenergic receptor binding / Activation of G protein gated Potassium channels / G-protein activation ...Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / sensory perception of chemical stimulus / Activation of the phototransduction cascade / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / beta-2 adrenergic receptor binding / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / spermatid development / D1 dopamine receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / insulin-like growth factor receptor binding / ionotropic glutamate receptor binding / adenylate cyclase activator activity / G protein-coupled receptor activity / G-protein beta/gamma-subunit complex binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / sensory perception of taste / signaling receptor complex adaptor activity / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / cell surface receptor signaling pathway / cell population proliferation / apical plasma membrane / G protein-coupled receptor signaling pathway / GTPase activity / synapse / GTP binding / protein-containing complex binding / metal ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
GAIN domain superfamily / GPCR proteolysis site, GPS, motif / : / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) ...GAIN domain superfamily / GPCR proteolysis site, GPS, motif / : / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / G-protein alpha subunit, group S / 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 / G protein beta WD-40 repeat protein / 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. / 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 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(s) subunit alpha / Adhesion G-protein coupled receptor G2
Similarity search - Component
Biological speciesBos taurus (domestic cattle) / Spodoptera (butterflies/moths)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsHuang SM / Sheng-chao G
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Chem Biol / Year: 2025
Title: Development of an allosteric adhesion GPCR nanobody with therapeutic potential.
Authors: Yuan Zheng / Dan Jiang / Yan Lu / Chao Zhang / Shen-Ming Huang / Haocheng Lin / Daolai Zhang / Shengchao Guo / Jifei Han / Jun Chen / Yaxuan He / Mingxiang Zhang / Yanhui Gao / Yongyuan Guo ...Authors: Yuan Zheng / Dan Jiang / Yan Lu / Chao Zhang / Shen-Ming Huang / Haocheng Lin / Daolai Zhang / Shengchao Guo / Jifei Han / Jun Chen / Yaxuan He / Mingxiang Zhang / Yanhui Gao / Yongyuan Guo / Ran Wei / Ming Xia / Yingying Qin / Zhaoqian Liu / Fan Yang / Shaohua Ge / Fan Yi / Xiao Yu / Hui Lin / Peng Xiao / Jin-Peng Sun / Shiqing Feng /
Abstract: Allosteric modulation of receptor responses to endogenous agonists has therapeutic value, maintaining ligand profiles, reducing side effects and restoring mutant responses. Adhesion G-protein-coupled ...Allosteric modulation of receptor responses to endogenous agonists has therapeutic value, maintaining ligand profiles, reducing side effects and restoring mutant responses. Adhesion G-protein-coupled receptors (aGPCRs), with large N termini, are ideal for allosteric modulator development. We designed a nanobody strategy targeting ADGRG2 N-terminal fragments and got a specific nanobody Nb23-bi, which promoted dehydroepiandrosterone (DHEA)-induced ADGRG2 activation and reversed mutant-induced dysfunctions. By combining structural characterization, crosslinking mass spectrometry, mutational analysis and molecular dynamics simulations, we clarified the allosteric mechanism of how the Nb23-bi modulates conformational changes in the DHEA-binding pocket. Animal studies showed that Nb23-bi promoted the response of DHEA in alleviating testicular inflammation and reversing mutant defects. In summary, we developed an allosteric nanobody of ADGRG2 and gained insights into its functions in reversing disease-associated dysfunctions. Our study may serve as a template for developing allosteric modulators of other aGPCRs for biological and therapeutic purposes.
History
DepositionMar 4, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39365.png

Downloads & links

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Map

FileDownload / File: emd_39365.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 250 pix.
= 262.5 Å		1.05 Å/pix.
x 250 pix.
= 262.5 Å		1.05 Å/pix.
x 250 pix.
= 262.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.0018191617 - 1.2592492
Average (Standard dev.)0.00101541 (±0.019341508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 262.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39365_half_map_1.map
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Half map: #1

Fileemd_39365_half_map_2.map
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Sample components

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Entire : Complex of ADGRG2 with nanonody and G protein trimer

EntireName: Complex of ADGRG2 with nanonody and G protein trimer
Components
  • Complex: Complex of ADGRG2 with nanonody and G protein trimer
    • Protein or peptide: Guanine nucleotide-binding protein G(s) 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 subunit gamma
    • Protein or peptide: Nanobody-35
    • Protein or peptide: Adhesion G-protein coupled receptor G2
    • Protein or peptide: ScFv-16
  • Ligand: 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE

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Supramolecule #1: Complex of ADGRG2 with nanonody and G protein trimer

SupramoleculeName: Complex of ADGRG2 with nanonody and G protein trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Bos taurus (domestic cattle)

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

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spodoptera (butterflies/moths)
Molecular weightTheoretical: 41.879465 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RATHRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RATHRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTSGIFETK FQVDKVNFHM FDVGAQRDER RKWIQCFNDV TAIIFVVDSS DYNRLQEALN DF KSIWNNR WLRTISVILF LNKQDLLAEK VLAGKSKIED YFPEFARYTT PEDATPEPGE DPRVTRAKYF IRDEFLRIST ASG DGRHYC YPHFTCSVDT ENARRIFNDC RDIIQRMHLR QYELL

UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha

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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: Spodoptera (butterflies/moths)
Molecular weightTheoretical: 39.418086 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
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

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

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Macromolecule #3: Guanine nucleotide-binding protein subunit gamma

MacromoleculeName: Guanine nucleotide-binding protein subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spodoptera (butterflies/moths)
Molecular weightTheoretical: 12.104898 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString:
MWRELPLGLG ELHKDHQASR KLEPELWSVS ENPPSTSMAS NNTASIAQAR KLVEQLKMEA NIDRIKVSKA AADLMAYCEA HAKEDPLLT PVPASENPFR EKKFFCAIL

UniProtKB: Guanine nucleotide-binding protein subunit gamma

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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: Spodoptera (butterflies/moths)
Molecular weightTheoretical: 13.885439 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString:
QVQLQESGGG LVQPGGSLRL SCAASGFTFS NYKMNWVRQA PGKGLEWVSD ISQSGASISY TGSVKGRFTI SRDNAKNTLY LQMNSLKPE DTAVYYCARC PAPFTRDCFD VTSTTYAYRG QGTQVTVSS

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Macromolecule #5: Adhesion G-protein coupled receptor G2

MacromoleculeName: Adhesion G-protein coupled receptor G2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spodoptera (butterflies/moths)
Molecular weightTheoretical: 98.934797 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MKTIIALSYI FCLVFADYKD DDDKLKENGN SSLLSPSAES SLVSLIPYSN GTPDAASEVL STLNKTEKSK ITIVKTFNAS GVKSQRNIC NLSSLCNDSV FFRGEIVFQH DEDHNVTQNQ DTANGTFAGV LSLSELKRSE LNKTLQTLSE TYFIVCATAE A QSTVNCTF ...String:
MKTIIALSYI FCLVFADYKD DDDKLKENGN SSLLSPSAES SLVSLIPYSN GTPDAASEVL STLNKTEKSK ITIVKTFNAS GVKSQRNIC NLSSLCNDSV FFRGEIVFQH DEDHNVTQNQ DTANGTFAGV LSLSELKRSE LNKTLQTLSE TYFIVCATAE A QSTVNCTF TVKLNETMNV CAMMVTFQTV QIRPMEQCCC SPRTPCPSSP EELEKLQCEL QDPIVCLADQ PHGPPLSSSS KP VVPQATI ISHVASDFSL AEPLDHALMT PSTPSLTQES NLPSPQPTIP LASSPATDLP VQSVVVSSLP QTDLSHTLSP VQS SIPSPT TPAPSVPTEL VTISTPPGET VVNTSTVSDL EAQVSQMEKA LSLGSLEPNL AGEMVNRVSK LLHSPPALLA PLAQ RLLKV VDAIGLQLNF SSTTISLTSP SLALAVIRVN ASNFNTTTFA AQDPTNLQVS LETPPPENSI GAITLPSSLM NNLPA NDVE LASRIQFNFF ETPALFQDPS LENLTLISYV ISSSVTNMTI KNLTRNVTVA LKHINPSPDD LTVKCVFWDL GRNGGK GGW SSDGCSVKDK RMNETICTCS ALASFGILLD LSRTSLPPSQ MMALTFITYI GCGLSSIFLS VTLVTYIAFE KIRRDYP SK ILIQLCAALL LLNLIFLLDS WIALYNTRGF CIAVAVFLHY FLLVSFTWMG LEAFHMYLAL VKVFNTYIRK YILKFCIV G WGIPAVVVSI VLTISPDNYG IGSYGKFPNG TPDDFCWINS NVVFYITVVG YFCVIFLLNV SMFIVVLVQL CRIKKKKQL GAQRKTSIQD LRSIAGLTFL LGITWGFAFF AWGPVNVTFM YLFAIFNTLQ GFFIFIFYCA AKENVRKQWR RYLCCGKLFW FPEKGAILT DTSVKRNDLS IISG

UniProtKB: Adhesion G-protein coupled receptor G2

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Macromolecule #6: ScFv-16

MacromoleculeName: ScFv-16 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spodoptera (butterflies/moths)
Molecular weightTheoretical: 26.640643 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGSSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGSSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KGS

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Macromolecule #7: 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE

MacromoleculeName: 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE / type: ligand / ID: 7 / Number of copies: 1 / Formula: AND
Molecular weightTheoretical: 288.424 Da
Chemical component information

ChemComp-AND:
3-BETA-HYDROXY-5-ANDROSTEN-17-ONE

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 241188
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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