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- EMDB-9911: cryo-EM structure of alpha2BAR-GoA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9911
Titlecryo-EM structure of alpha2BAR-GoA complex
Map dataalpha2BAR-GoA complex
Sample
  • Complex: alpha2BAR-GoA complex
    • Protein or peptide: Guanine nucleotide-binding protein G(o) 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: 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
Function / homology
Function and homology information


Adrenoceptors / Adrenaline signalling through Alpha-2 adrenergic receptor / Surfactant metabolism / regulation of vascular associated smooth muscle contraction / Activation of the phototransduction cascade / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / alpha2-adrenergic receptor activity / Adrenaline signalling through Alpha-2 adrenergic receptor / G beta:gamma signalling through PLC beta ...Adrenoceptors / Adrenaline signalling through Alpha-2 adrenergic receptor / Surfactant metabolism / regulation of vascular associated smooth muscle contraction / Activation of the phototransduction cascade / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / alpha2-adrenergic receptor activity / Adrenaline signalling through Alpha-2 adrenergic receptor / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Prostacyclin signalling through prostacyclin receptor / G alpha (z) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / receptor transactivation / epinephrine binding / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G beta:gamma signalling through BTK / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / positive regulation of uterine smooth muscle contraction / negative regulation of norepinephrine secretion / Thrombin signalling through proteinase activated receptors (PARs) / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Ca2+ pathway / G alpha (s) signalling events / negative regulation of epinephrine secretion / G alpha (q) signalling events / Extra-nuclear estrogen signaling / G alpha (12/13) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / regulation of smooth muscle contraction / ADP signalling through P2Y purinoceptor 1 / mu-type opioid receptor binding / phototransduction, visible light / corticotropin-releasing hormone receptor 1 binding / positive regulation of blood pressure / vesicle docking involved in exocytosis / Adrenoceptors / Adrenaline,noradrenaline inhibits insulin secretion / alkylglycerophosphoethanolamine phosphodiesterase activity / G alpha (z) signalling events / photoreceptor outer segment membrane / G alpha (i) signalling events / G protein-coupled dopamine receptor signaling pathway / regulation of heart contraction / spectrin binding / adrenergic receptor signaling pathway / photoreceptor outer segment / regulation of vasoconstriction / negative regulation of insulin secretion / G protein-coupled serotonin receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / viral release from host cell by cytolysis / cardiac muscle cell apoptotic process / muscle contraction / positive regulation of neuron differentiation / activation of protein kinase B activity / photoreceptor inner segment / peptidoglycan catabolic process / female pregnancy / locomotory behavior / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / platelet activation / 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 / 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 / MAPK cascade
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 / 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) / Lysozyme-like domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Endolysin / Guanine nucleotide-binding protein G(o) subunit alpha / 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 / Alpha-2A adrenergic receptor
Similarity search - Component
Biological speciesSpodoptera (butterflies/moths) / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYuan D / Liu Z / Wang HW / Kobilka BK
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-
UpdateMay 13, 2020-
Current statusMay 13, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0151
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0151
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6k41
  • Surface level: 0.0151
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9911.png

Downloads & links

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Map

FileDownload / File: emd_9911.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationalpha2BAR-GoA complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.55 Å/pix.
x 400 pix.
= 218.2 Å		0.55 Å/pix.
x 400 pix.
= 218.2 Å		0.55 Å/pix.
x 400 pix.
= 218.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5455 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0151 / Movie #1: 0.0151
Minimum - Maximum-0.10227652 - 0.16358423
Average (Standard dev.)0.00006958078 (±0.0029199512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 218.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.54550.54550.5455
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z218.200218.200218.200
α/β/γ90.00090.00090.000
start NX/NY/NZ636181
NX/NY/NZ13113592
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1020.1640.000

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Supplemental data

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Sample components

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Entire : alpha2BAR-GoA complex

EntireName: alpha2BAR-GoA complex
Components
  • Complex: alpha2BAR-GoA complex
    • Protein or peptide: Guanine nucleotide-binding protein G(o) 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: 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-GoA complex

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

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

MacromoleculeName: Guanine nucleotide-binding protein G(o) subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.1005 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MGCTLSAEER AALERSKAIE KNLKEDGISA AKDVKLLLLG AGESGKSTIV KQMKIIHEDG FSGEDVKQYK PVVYSNTIQS LAAIVRAMD TLGIEYGDKE RKADAKMVCD VVSRMEDTEP FSAELLSAMM RLWGDSGIQE CFNRSREYQL NDSAKYYLDS L DRIGAADY ...String:
MGCTLSAEER AALERSKAIE KNLKEDGISA AKDVKLLLLG AGESGKSTIV KQMKIIHEDG FSGEDVKQYK PVVYSNTIQS LAAIVRAMD TLGIEYGDKE RKADAKMVCD VVSRMEDTEP FSAELLSAMM RLWGDSGIQE CFNRSREYQL NDSAKYYLDS L DRIGAADY QPTEQDILRT RVKTTGIVET HFTFKNLHFR LFDVGGQRSE RKKWIHCFED VTAIIFCVAL SGYDQVLHED ET TNRMHES LMLFDSICNN KFFIDTSIIL FLNKKDLFGE KIKKSPLTIC FPEYTGPNTY EDAAAYIQAQ FESKNRSPNK EIY CHMTCA TDTNNIQVVF DAVTDIIIAN NLRGCGLY

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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: 38.402867 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: HHHHHHGSSG SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLI IWDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR F LDDNQIVT ...String:
HHHHHHGSSG SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLI IWDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR F LDDNQIVT SSGDTTCALW DIETGQQTTT FTGHTGDVMS LSLAPDTRLF VSGACDASAK LWDVREGMCR QTFTGHESDI NA ICFFPNG NAFATGSDDA TCRLFDLRAD QELMTYSHDN IICGITSVSF SKSGRLLLAG YDDFNCNVWD ALKADRAGVL AGH DNRVSC LGVTDDGMAV ATGSWDSFLK IWN

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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

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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

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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 stateparticle

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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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 258283
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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