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- EMDB-33249: Cryo-EM structure of DHEA-ADGRG2-FL-Gs complex -

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Entry
Database: EMDB / ID: EMD-33249
TitleCryo-EM structure of DHEA-ADGRG2-FL-Gs complex
Map dataThe cryo-em density of DHEA-ADGRG2-FL-Gs complex
Sample
  • Complex: Adhesion G-protein coupled receptor G2
    • Protein or peptide: mini-Gs
    • 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: NB35
    • Protein or peptide: Adhesion G-protein coupled receptor G2
  • Ligand: 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE
  • Ligand: water
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 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / apical plasma membrane / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GPS 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 ...GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GPS 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, 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
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 / Adhesion G-protein coupled receptor G2
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human) / Camelus bactrianus (Bactrian camel)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsGuo SC / Xiao P / Lin H / Sun JP / Yu X
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92057121 China
National Natural Science Foundation of China (NSFC)32130055 China
National Science Foundation (NSF, China)81825022 China
National Natural Science Foundation of China (NSFC)ZR2021ZD18 China
CitationJournal: Nat Chem Biol / Year: 2022
Title: Structures of the ADGRG2-G complex in apo and ligand-bound forms.
Authors: Hui Lin / Peng Xiao / Rui-Qian Bu / Shengchao Guo / Zhao Yang / Daopeng Yuan / Zhong-Liang Zhu / Chuan-Xin Zhang / Qing-Tao He / Chao Zhang / Yu-Qi Ping / Ru-Jia Zhao / Chuan-Shun Ma / Chang- ...Authors: Hui Lin / Peng Xiao / Rui-Qian Bu / Shengchao Guo / Zhao Yang / Daopeng Yuan / Zhong-Liang Zhu / Chuan-Xin Zhang / Qing-Tao He / Chao Zhang / Yu-Qi Ping / Ru-Jia Zhao / Chuan-Shun Ma / Chang-Hao Liu / Xiao-Ning Zhang / Dan Jiang / Shaohui Huang / Yue-Tong Xi / Dao-Lai Zhang / Chen-Yang Xue / Bai-Sheng Yang / Jian-Yuan Li / Hao-Cheng Lin / Xu-Hui Zeng / Han Zhao / Wen-Ming Xu / Fan Yi / Zhongmin Liu / Jin-Peng Sun / Xiao Yu /
Abstract: Adhesion G protein-coupled receptors are elusive in terms of their structural information and ligands. Here, we solved the cryogenic-electron microscopy (cryo-EM) structure of apo-ADGRG2, an ...Adhesion G protein-coupled receptors are elusive in terms of their structural information and ligands. Here, we solved the cryogenic-electron microscopy (cryo-EM) structure of apo-ADGRG2, an essential membrane receptor for maintaining male fertility, in complex with a G trimer. Whereas the formations of two kinks were determinants of the active state, identification of a potential ligand-binding pocket in ADGRG2 facilitated the screening and identification of dehydroepiandrosterone (DHEA), dehydroepiandrosterone sulfate and deoxycorticosterone as potential ligands of ADGRG2. The cryo-EM structures of DHEA-ADGRG2-G provided interaction details for DHEA within the seven transmembrane domains of ADGRG2. Collectively, our data provide a structural basis for the activation and signaling of ADGRG2, as well as characterization of steroid hormones as ADGRG2 ligands, which might be used as useful tools for further functional studies of the orphan ADGRG2.
History
DepositionApr 19, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateMar 15, 2023-
Current statusMar 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33249.png

Downloads & links

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Map

FileDownload / File: emd_33249.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryo-em density of DHEA-ADGRG2-FL-Gs complex
Voxel sizeX=Y=Z: 1.052 Å
Density
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.038264092 - 0.078221634
Average (Standard dev.)5.3896532e-05 (±0.0021388137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 263.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: The half2 map of DHEA-ADGRG2-FL-Gs complex

Fileemd_33249_half_map_1.map
AnnotationThe half2 map of DHEA-ADGRG2-FL-Gs complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half1 map of DHEA-ADGRG2-FL-Gs complex

Fileemd_33249_half_map_2.map
AnnotationThe half1 map of DHEA-ADGRG2-FL-Gs complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Adhesion G-protein coupled receptor G2

EntireName: Adhesion G-protein coupled receptor G2
Components
  • Complex: Adhesion G-protein coupled receptor G2
    • Protein or peptide: mini-Gs
    • 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: NB35
    • Protein or peptide: Adhesion G-protein coupled receptor G2
  • Ligand: 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE
  • Ligand: water

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Supramolecule #1: Adhesion G-protein coupled receptor G2

SupramoleculeName: Adhesion G-protein coupled receptor G2 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: mini-Gs

MacromoleculeName: mini-Gs / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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

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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: 39.48916 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MHHHHHHLEV LFQGPGSSQS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR ...String:
MHHHHHHLEV LFQGPGSSQS 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: 6.375332 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString:
NTASIAQARK LVEQLKMEAN IDRIKVSKAA ADLMAYCEAH AKEDPLLTPV PASENPFR

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Macromolecule #4: NB35

MacromoleculeName: NB35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Camelus bactrianus (Bactrian camel)
Molecular weightTheoretical: 13.885439 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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
Details: C-terminal(892-916) is due to the replacement of GPR120 tail.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
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

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Macromolecule #6: 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE

MacromoleculeName: 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE / type: ligand / ID: 6 / Number of copies: 1 / Formula: AND
Molecular weightTheoretical: 288.424 Da
Chemical component information

ChemComp-AND:
3-BETA-HYDROXY-5-ANDROSTEN-17-ONE / hormone*YM / Dehydroepiandrosterone

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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 TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 IS (4k x 4k) / Average electron dose: 58.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 238405

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