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- EMDB-9912: cryo-EM structure of alpha2BAR-Gi1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9912
Titlecryo-EM structure of alpha2BAR-Gi1 complex
Map dataalpha2BAR-Gi1 complex
Sample
  • Complex: alpha2BAR-Gi1 complex
    • 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
    • Protein or peptide: Alpha-2A adrenergic receptor,Endolysin,Alpha-2B adrenergic receptor,Alpha-2B adrenergic receptor
    • Protein or peptide: scFv
  • Ligand: 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole
KeywordsGPCR / Complex / cryo-EM / MEMBRANE PROTEIN
Function / homology
Function and homology information


Activation of the phototransduction cascade / Olfactory Signaling Pathway / negative regulation of uterine smooth muscle contraction / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / Prostacyclin signalling through prostacyclin receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / alpha2-adrenergic receptor activity / Adrenaline signalling through Alpha-2 adrenergic receptor ...Activation of the phototransduction cascade / Olfactory Signaling Pathway / negative regulation of uterine smooth muscle contraction / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / Prostacyclin signalling through prostacyclin receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / alpha2-adrenergic receptor activity / Adrenaline signalling through Alpha-2 adrenergic receptor / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G alpha (z) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / alpha-2C adrenergic receptor binding / epinephrine binding / positive regulation of uterine smooth muscle contraction / Adrenaline,noradrenaline inhibits insulin secretion / phospholipase C-activating adrenergic receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G beta:gamma signalling through BTK / Adenylate cyclase inhibitory pathway / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / alpha-1B adrenergic receptor binding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / negative regulation of norepinephrine secretion / G-protein activation / G alpha (s) signalling events / negative regulation of epinephrine secretion / Ca2+ pathway / G alpha (12/13) signalling events / Extra-nuclear estrogen signaling / G alpha (q) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / regulation of vascular associated smooth muscle contraction / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / heterotrimeric G-protein binding / G alpha (i) signalling events / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / ADP signalling through P2Y purinoceptor 1 / negative regulation of calcium ion-dependent exocytosis / positive regulation of blood pressure / Surfactant metabolism / positive regulation of potassium ion transport / dopaminergic synapse / thermoception / fear response / thioesterase binding / negative regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of membrane protein ectodomain proteolysis / norepinephrine binding / Adrenoceptors / response to alcohol / intestinal absorption / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / positive regulation of epidermal growth factor receptor signaling pathway / response to morphine / Extra-nuclear estrogen signaling / positive regulation of wound healing / adrenergic receptor signaling pathway / spectrin binding / G alpha (i) signalling events / alkylglycerophosphoethanolamine phosphodiesterase activity / negative regulation of calcium ion transport / phototransduction, visible light / photoreceptor outer segment / regulation of vasoconstriction / negative regulation of lipid catabolic process / viral release from host cell by cytolysis / cellular response to hormone stimulus / positive regulation of protein localization to cell cortex / Rho protein signal transduction / adenylate cyclase-activating adrenergic receptor signaling pathway / G protein-coupled serotonin receptor binding / presynaptic active zone membrane / axon terminus / peptidoglycan catabolic process / cardiac muscle cell apoptotic process / positive regulation of neuron differentiation / presynaptic modulation of chemical synaptic transmission / cellular response to forskolin / regulation of mitotic spindle organization / guanyl-nucleotide exchange factor activity / positive regulation of cytokine production / negative regulation of insulin secretion / female pregnancy / G protein-coupled receptor binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / postsynaptic density membrane / GABA-ergic synapse / platelet activation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / vasodilation
Similarity search - Function
Alpha 2B adrenoceptor / Alpha 2A adrenoceptor / Adrenoceptor family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / G-protein alpha subunit, group I ...Alpha 2B adrenoceptor / Alpha 2A adrenoceptor / Adrenoceptor family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / 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 coupled receptors family 1 signature. / Lysozyme-like domain superfamily / 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. / 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
Endolysin / Alpha-2A adrenergic receptor / Alpha-2B adrenergic receptor / 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
Similarity search - Component
Biological speciesSpodoptera (butterflies/moths) / Bos taurus (domestic cattle) / Mus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsYuan D / Liu Z
CitationJournal: Nat Chem Biol / Year: 2020
Title: Activation of the α adrenoceptor by the sedative sympatholytic dexmedetomidine.
Authors: Daopeng Yuan / Zhongmin Liu / Jonas Kaindl / Shoji Maeda / Jiawei Zhao / Xiaoou Sun / Jun Xu / Peter Gmeiner / Hong-Wei Wang / Brian K Kobilka /
Abstract: The α adrenergic receptors (αARs) are G protein-coupled receptors (GPCRs) that respond to adrenaline and noradrenaline and couple to the Gi/o family of G proteins. αARs play important roles in ...The α adrenergic receptors (αARs) are G protein-coupled receptors (GPCRs) that respond to adrenaline and noradrenaline and couple to the Gi/o family of G proteins. αARs play important roles in regulating the sympathetic nervous system. Dexmedetomidine is a highly selective αAR agonist used in post-operative patients as an anxiety-reducing, sedative medicine that decreases the requirement for opioids. As is typical for selective αAR agonists, dexmedetomidine consists of an imidazole ring and a substituted benzene moiety lacking polar groups, which is in contrast to βAR-selective agonists, which share an ethanolamine group and an aromatic system with polar, hydrogen-bonding substituents. To better understand the structural basis for the selectivity and efficacy of adrenergic agonists, we determined the structure of the αAR in complex with dexmedetomidine and Go at a resolution of 2.9 Å by single-particle cryo-EM. The structure reveals the mechanism of αAR-selective activation and provides insights into Gi/o coupling specificity.
History
DepositionMay 23, 2019-
Header (metadata) releaseApr 15, 2020-
Map releaseApr 15, 2020-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.131
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.131
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6k42
  • Surface level: 0.131
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9912.png

Downloads & links

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Map

FileDownload / File: emd_9912.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationalpha2BAR-Gi1 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 240 pix.
= 336.24 Å		1.4 Å/pix.
x 240 pix.
= 336.24 Å		1.4 Å/pix.
x 240 pix.
= 336.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.401 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.131 / Movie #1: 0.131
Minimum - Maximum-0.5579599 - 0.7024254
Average (Standard dev.)0.00024739938 (±0.009728292)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 336.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4011.4011.401
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z336.240336.240336.240
α/β/γ90.00090.00090.000
start NX/NY/NZ636181
NX/NY/NZ13113592
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.5580.7020.000

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Supplemental data

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Sample components

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Entire : alpha2BAR-Gi1 complex

EntireName: alpha2BAR-Gi1 complex
Components
  • Complex: alpha2BAR-Gi1 complex
    • 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
    • Protein or peptide: Alpha-2A adrenergic receptor,Endolysin,Alpha-2B adrenergic receptor,Alpha-2B adrenergic receptor
    • Protein or peptide: scFv
  • Ligand: 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole

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Supramolecule #1: alpha2BAR-Gi1 complex

SupramoleculeName: alpha2BAR-Gi1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Spodoptera (butterflies/moths)
Molecular weightTheoretical: 150 KDa

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

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 40.415031 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGGQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHESM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCA TDTKNVQFVF DAVTDVIIKN NLKDCGLF

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

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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: Mus musculus (house mouse)
Molecular weightTheoretical: 38.530992 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: HHHHHHGSSG QSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC R FLDDNQIV ...String:
HHHHHHGSSG QSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC R FLDDNQIV TSSGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD IN AICFFPN GNAFATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAG HDNRVS CLGVTDDGMA VATGSWDSFL KIWN

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

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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: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
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 #4: Alpha-2A adrenergic receptor,Endolysin,Alpha-2B adrenergic recept...

MacromoleculeName: Alpha-2A adrenergic receptor,Endolysin,Alpha-2B adrenergic receptor,Alpha-2B adrenergic receptor
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: lysozyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.156211 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: DDDDAHHHHH HMGSLQPDAG NASWNGTEAP GGGARATPEN LYFQGNIFEM LRIDEGLRLK IYKDTEGYYT IGIGHLLTKS PSLNAAKSE LDKAIGRNTN GVITKDEAEK LFNQDVDAAV RGILRNAKLK PVYDSLDAVR RAALINMVFQ MGETGVAGFT N SLRMLQQK ...String:
DDDDAHHHHH HMGSLQPDAG NASWNGTEAP GGGARATPEN LYFQGNIFEM LRIDEGLRLK IYKDTEGYYT IGIGHLLTKS PSLNAAKSE LDKAIGRNTN GVITKDEAEK LFNQDVDAAV RGILRNAKLK PVYDSLDAVR RAALINMVFQ MGETGVAGFT N SLRMLQQK RWDEAAVNLA KSRWYNQTPN RAKRVITTFR TGTWDAYYSV QATAAIAAAI TFLILFTIFG NALVILAVLT SR SLRAPQN LFLVSLAAAD ILVATLIIPF SLANELLGYW YFRRTWCEVY LALDVLFCTS SIVHLCAISL DRYWAVSRAL EYN SKRTPR RIKCIILTVW LIAAVISLPP LIYKGDQGPQ PRGRPQCKLN QEAWYILASS IGSFFAPCLI MILVYLRIYL IAKR SNRRG PRAKGGPGQG EQWWRRRAQL TREKRFTFVL AVVIGVFVLC WFPFFFSYSL GAICPKHCKV PHGLFQFFFW IGYCN SSLN PVIYTIFNQD FRRAFRRILC RPWTQTAW

UniProtKB: Alpha-2A adrenergic receptor, Endolysin, Alpha-2B adrenergic receptor, Alpha-2B adrenergic receptor

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Macromolecule #5: scFv

MacromoleculeName: scFv / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 32.898781 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFADV QLVESGGGLV QPGGSRKLSC SASGFAFSSF GMHWVRQAPE KGLEWVAYI SSGSGTIYYA DTVKGRFTIS RDDPKNTLFL QMTSLRSEDT AMYYCVRSIY YYGSSPFDFW GQGTTLTVSS G GGGSGGGG ...String:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFADV QLVESGGGLV QPGGSRKLSC SASGFAFSSF GMHWVRQAPE KGLEWVAYI SSGSGTIYYA DTVKGRFTIS RDDPKNTLFL QMTSLRSEDT AMYYCVRSIY YYGSSPFDFW GQGTTLTVSS G GGGSGGGG SGGGGSDIVM TQATSSVPVT PGESVSISCR SSKSLLHSNG NTYLYWFLQR PGQSPQLLIY RMSNLASGVP DR FSGSGSG TAFTLTISRL EAEDVGVYYC MQHLEYPLTF GAGTKLELKG SLEVLFQGPA AAHHHHHHHH

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Macromolecule #6: 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole

MacromoleculeName: 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole
type: ligand / ID: 6 / Number of copies: 1 / Formula: CZX
Molecular weightTheoretical: 200.28 Da
Chemical component information

ChemComp-CZX:
4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole

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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

Concentration10 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 235982
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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