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- EMDB-61745: GABA-DGABAB-Gi-complex -

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Basic information

Entry
Database: EMDB / ID: EMD-61745
TitleGABA-DGABAB-Gi-complex
Map data
Sample
  • Complex: DGABAB-Gi
    • Protein or peptide: Metabotropic GABA-B receptor subtype 1
    • Protein or peptide: Gamma-aminobutyric acid type B receptor subunit 2
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • 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
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
KeywordsGPCR / DGABAB / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of synaptic vesicle fusion to presynaptic active zone membrane / olfactory behavior / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / gamma-aminobutyric acid signaling pathway / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / Adenylate cyclase inhibitory pathway / T cell migration / D2 dopamine receptor binding ...negative regulation of synaptic vesicle fusion to presynaptic active zone membrane / olfactory behavior / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / gamma-aminobutyric acid signaling pathway / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / Adenylate cyclase inhibitory pathway / T cell migration / D2 dopamine receptor binding / response to prostaglandin E / adenylate cyclase regulator activity / G protein-coupled serotonin receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / cellular response to forskolin / regulation of mitotic spindle organization / Regulation of insulin secretion / positive regulation of cholesterol biosynthetic process / negative regulation of insulin secretion / cellular response to mechanical stimulus / G protein-coupled receptor binding / response to peptide hormone / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / centriolar satellite / 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 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / GDP binding / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / 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) / retina development in camera-type eye / G protein activity / GTPase binding / Ca2+ pathway / fibroblast proliferation / midbody / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / cell cortex / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Ras protein signal transduction / Extra-nuclear estrogen signaling / cell population proliferation / ciliary basal body / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / synapse / centrosome / GTP binding / protein-containing complex binding / nucleolus / magnesium ion binding / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GPCR family 3, gamma-aminobutyric acid receptor, type B1 / GPCR family 3, GABA-B receptor / G-protein coupled receptors family 3 signature 3. / GPCR, family 3, conserved site / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein alpha subunit, group I / Receptor, ligand binding region / Receptor family ligand binding region ...GPCR family 3, gamma-aminobutyric acid receptor, type B1 / GPCR family 3, GABA-B receptor / G-protein coupled receptors family 3 signature 3. / GPCR, family 3, conserved site / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein alpha subunit, group I / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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 G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Gamma-aminobutyric acid type B receptor subunit 2 / Metabotropic GABA-B receptor subtype 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
Authorsshen CS / liu JF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural basis of GABAB receptor activation during evolution
Authors: shen CS / liu JF
History
DepositionSep 28, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61745.png

Downloads & links

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Map

FileDownload / File: emd_61745.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0039
Minimum - Maximum-0.034617223 - 0.056582812
Average (Standard dev.)0.000014014673 (±0.001299439)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 297.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61745_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_61745_half_map_1.map
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Half map: #1

Fileemd_61745_half_map_2.map
Projections & Slices
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Sample components

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Entire : DGABAB-Gi

EntireName: DGABAB-Gi
Components
  • Complex: DGABAB-Gi
    • Protein or peptide: Metabotropic GABA-B receptor subtype 1
    • Protein or peptide: Gamma-aminobutyric acid type B receptor subunit 2
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • 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
  • Ligand: GAMMA-AMINO-BUTANOIC ACID

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Supramolecule #1: DGABAB-Gi

SupramoleculeName: DGABAB-Gi / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Metabotropic GABA-B receptor subtype 1

MacromoleculeName: Metabotropic GABA-B receptor subtype 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 88.52825 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GVAGRPDELH IGGIFPIAGK GGWQGGQACM PATRLALDDV NKQPNLLPGF KLILHSNDSE CEPGLGASVM YNLLYNKPQK LMLLAGCST VCTTVAEAAK MWNLIVLCYG ASSPALSDRK RFPTLFRTHP SATVHNPTRI KLMKKFGWSR VAILQQAEEV F ISTVEDLE ...String:
GVAGRPDELH IGGIFPIAGK GGWQGGQACM PATRLALDDV NKQPNLLPGF KLILHSNDSE CEPGLGASVM YNLLYNKPQK LMLLAGCST VCTTVAEAAK MWNLIVLCYG ASSPALSDRK RFPTLFRTHP SATVHNPTRI KLMKKFGWSR VAILQQAEEV F ISTVEDLE NRCMEAGVEI VTRQSFLSDP TDAVRNLRRQ DARIIVGLFY VVAARRVLCE MYKQQLYGRA HVWFFIGWYE DN WYEVNLK AEGITCTVEQ MRIAAEGHLT TEALMWNQNN QTTISGMTAE EFRHRLNQAL IEEGYDINHD RYPEGYQEAP LAY DAVWSV ALAFNKTMER LTTGKKSLRD FTYTDKEIAD EIYAAMNSTQ FLGVSGVVAF SSQGDRIALT QIEQMIDGKY EKLG YYDTQ LDNLSWLNTE QWIGGKVPQD RTIVTHVLRT VSLPLFVCMC TISSCGIFVA FALIIFNIWN KHRRVIQSSH PVCNT IMLF GVIICLISVI LLGIDGRFVS PEEYPKICQA RAWLLSTGFT LAYGAMFSKV WRVHRFTTKA KTDPKKKVEP WKLYTM VSG LLSIDLVILL SWQIFDPLQR YLETFPLEDP VSTTDDIKIR PELEHCESQR NSMWLGLVYG FKGLILVFGL FLAYETR SI KVKQINDSRY VGMSIYNVVV LCLITAPVGM VIASQQDASF AFVALAVIFC CFLSMLLIFV PKVIEVIRHP KDKAESKY N PDSAISKEDE ERYQKLVTEN EQLQRLITQK EEKIRVLRQR LVERGDAKGT ELEVLFQGP

UniProtKB: Metabotropic GABA-B receptor subtype 1

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Macromolecule #2: Gamma-aminobutyric acid type B receptor subunit 2

MacromoleculeName: Gamma-aminobutyric acid type B receptor subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 87.493703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RTAKRSDVYI AGFFPYGDGV ENSYTGRGVM PSVKLALGHV NEHGKILANY RLHMWWNDTQ CNAAVGVKSF FDMMHSGPNK VMLFGAACT HVTDPIAKAS KHWHLTQLSY ADTHPMFTKD AFPNFFRVVP SENAFNAPRL ALLKEFNWTR VGTVYQNEPR Y SLPHNHMV ...String:
RTAKRSDVYI AGFFPYGDGV ENSYTGRGVM PSVKLALGHV NEHGKILANY RLHMWWNDTQ CNAAVGVKSF FDMMHSGPNK VMLFGAACT HVTDPIAKAS KHWHLTQLSY ADTHPMFTKD AFPNFFRVVP SENAFNAPRL ALLKEFNWTR VGTVYQNEPR Y SLPHNHMV ADLDAMEVEV VETQSFVNDV AESLKKLREK DVRIILGNFN EHFARKAFCE AYKLDMYGRA YQWLIMATYS TD WWNVTQD SECSVEEIAT ALEGAILVDL LPLSTSGDIT VAGITADEYL VEYDRLRGTE YSRFHGYTYD GIWAAALAIQ YVA EKREDL LTHFDYRVKD WESVFLEALR NTSFEGVTGP VRFYNNERKA NILINQFQLG QMEKIGEYHS QKSHLDLSLG KPVK WVGKT PPKDRTLIYI EHSQVNPTIY IVSASASVIG VIIATVFLAF NIKYRNQRYI KMSSPHLNNL IIVGCMITYL SIIFL GLDT TLSSVAAFPY ICTARAWILM AGFSLSFGAM FSKTWRVHSI FTDLKLNKKV IKDYQLFMVV GVLLAIDIAI ITTWQI ADP FYRETKQLEP LHHENIDDVL VIPENEYCQS EHMTIFVSII YAYKGLLLVF GAFLAWETRH VSIPALNDSK HIGFSVY NV FITCLAGAAI SLVLSDRKDL VFVLLSFFII FCTTATLCLV FVPKLVELKR NPQGVVDKRV RATLRPMSKN GRRDSSVC E LEQRLRDVKN TNCRFRKALM EKENELQALI RKLGPEARKW IDGVTC

UniProtKB: Gamma-aminobutyric acid type B receptor subunit 2

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Macromolecule #3: Guanine nucleotide-binding protein G(i) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.414047 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKNTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKNTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGAQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHASM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCS TDTKNVQFVF DAVTDVIIKN NLKDCGLF

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1

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Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.418086 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #5: 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: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

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

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Macromolecule #6: GAMMA-AMINO-BUTANOIC ACID

MacromoleculeName: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: ABU
Molecular weightTheoretical: 103.12 Da
Chemical component information

ChemComp-ABU:
GAMMA-AMINO-BUTANOIC ACID

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 7.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Polara / 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: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 558947
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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