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- EMDB-41267: Cryo-EM structure of A61603-bound alpha-1A-adrenergic receptor in... -

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Entry
Database: EMDB / ID: EMD-41267
TitleCryo-EM structure of A61603-bound alpha-1A-adrenergic receptor in complex with heterotrimeric Gq-protein
Map data
Sample
  • Complex: A61603-bound alpha-1A-adrenergic receptor in complex with heterotrimeric Gq-protein
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(q) 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: Single fab chain (scFv16)
    • Protein or peptide: Endolysin,Alpha-1A adrenergic receptor
  • Ligand: N-[(5S)-5-(4,5-dihydro-1H-imidazol-2-yl)-2-hydroxy-5,6,7,8-tetrahydronaphthalen-1-yl]methanesulfonamide
KeywordsAlpha-1A-adrenergic receptor / A61603 / SIGNALING PROTEIN
Function / homology
Function and homology information


negative regulation of heart rate involved in baroreceptor response to increased systemic arterial blood pressure / alpha1-adrenergic receptor activity / norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure / positive regulation of heart rate by epinephrine-norepinephrine / positive regulation of the force of heart contraction by epinephrine-norepinephrine / pilomotor reflex / phospholipase C-activating adrenergic receptor signaling pathway / neuron-glial cell signaling / sensory perception of itch / cell growth involved in cardiac muscle cell development ...negative regulation of heart rate involved in baroreceptor response to increased systemic arterial blood pressure / alpha1-adrenergic receptor activity / norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure / positive regulation of heart rate by epinephrine-norepinephrine / positive regulation of the force of heart contraction by epinephrine-norepinephrine / pilomotor reflex / phospholipase C-activating adrenergic receptor signaling pathway / neuron-glial cell signaling / sensory perception of itch / cell growth involved in cardiac muscle cell development / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / positive regulation of action potential / positive regulation of smooth muscle contraction / PLC beta mediated events / phospholipase C-activating serotonin receptor signaling pathway / negative regulation of calcium ion-dependent exocytosis / regulation of platelet activation / entrainment of circadian clock / G protein-coupled adenosine receptor signaling pathway / negative regulation of adenylate cyclase activity / adult heart development / negative regulation of synaptic transmission / positive regulation of neural precursor cell proliferation / Adrenoceptors / regulation of canonical Wnt signaling pathway / positive regulation of urine volume / cellular response to acidic pH / glutamate receptor signaling pathway / mast cell degranulation / positive regulation of cardiac muscle hypertrophy / gamma-aminobutyric acid signaling pathway / regulation of calcium ion transport / smooth muscle contraction / positive regulation of vasoconstriction / phototransduction, visible light / negative regulation of apoptotic signaling pathway / PKA activation in glucagon signalling / developmental growth / hair follicle placode formation / photoreceptor outer segment / intracellular transport / D1 dopamine receptor binding / postsynaptic cytosol / neuronal dense core vesicle / viral release from host cell by cytolysis / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / Hedgehog 'off' state / activation of adenylate cyclase activity / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of superoxide anion generation / adenylate cyclase-activating adrenergic receptor signaling pathway / response to hormone / Adenylate cyclase inhibitory pathway / peptidoglycan catabolic process / response to prostaglandin E / hormone-mediated signaling pathway / positive regulation of cardiac muscle contraction / response to nutrient / regulation of insulin secretion / cellular response to glucagon stimulus / negative regulation of autophagy / GTPase activator activity / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / adenylate cyclase activator activity / hippocampal mossy fiber to CA3 synapse / trans-Golgi network membrane / positive regulation of synaptic transmission, GABAergic / neuropeptide signaling pathway / negative regulation of inflammatory response to antigenic stimulus / Regulation of insulin secretion / G protein-coupled receptor binding / bone development / caveola / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / platelet aggregation / cognition / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / cell wall macromolecule catabolic process / Activation of the phototransduction cascade / blood coagulation / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / 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 activation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / lysozyme / G beta:gamma signalling through BTK / lysozyme activity / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12
Similarity search - Function
Alpha 1A adrenoceptor / G-protein alpha subunit, group Q / Adrenoceptor family / G-protein alpha subunit, group S / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily ...Alpha 1A adrenoceptor / G-protein alpha subunit, group Q / Adrenoceptor family / G-protein alpha subunit, group S / 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 / Lysozyme-like domain superfamily / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 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
Endolysin / Guanine nucleotide-binding protein G(i) subunit alpha-2 / Alpha-1A adrenergic receptor / Guanine nucleotide-binding protein G(q) subunit alpha / 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(s) subunit alpha isoforms short
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsSu M / Huang XY
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138676 United States
American Heart Association23CDA1049353 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis of agonist specificity of α-adrenergic receptor.
Authors: Minfei Su / Jinan Wang / Guoqing Xiang / Hung Nguyen Do / Joshua Levitz / Yinglong Miao / Xin-Yun Huang /
Abstract: α-adrenergic receptors (α-ARs) play critical roles in the cardiovascular and nervous systems where they regulate blood pressure, cognition, and metabolism. However, the lack of specific agonists ...α-adrenergic receptors (α-ARs) play critical roles in the cardiovascular and nervous systems where they regulate blood pressure, cognition, and metabolism. However, the lack of specific agonists for all α subtypes has limited our understanding of the physiological roles of different α-AR subtypes, and led to the stagnancy in agonist-based drug development for these receptors. Here we report cryo-EM structures of α-AR in complex with heterotrimeric G-proteins and either the endogenous common agonist epinephrine or the α-AR-specific synthetic agonist A61603. These structures provide molecular insights into the mechanisms underlying the discrimination between α-AR and α-AR by A61603. Guided by the structures and corresponding molecular dynamics simulations, we engineer α-AR mutants that are not responsive to A61603, and α-AR mutants that can be potently activated by A61603. Together, these findings advance our understanding of the agonist specificity for α-ARs at the molecular level, opening the possibility of rational design of subtype-specific agonists.
History
DepositionJul 17, 2023-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41267.png

Downloads & links

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Map

FileDownload / File: emd_41267.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesX (Sec.)Y (Row.)Z (Col.)
0.86 Å/pix.
x 320 pix.
= 273.92 Å		0.86 Å/pix.
x 320 pix.
= 273.92 Å		0.86 Å/pix.
x 320 pix.
= 273.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-32.950164999999998 - 64.932940000000002
Average (Standard dev.)-0.003209108 (±1.0803775)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Receptor and Ga focused map

Fileemd_41267_additional_1.map
AnnotationReceptor and Ga focused map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_41267_half_map_1.map
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Half map: #1

Fileemd_41267_half_map_2.map
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Sample components

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Entire : A61603-bound alpha-1A-adrenergic receptor in complex with heterot...

EntireName: A61603-bound alpha-1A-adrenergic receptor in complex with heterotrimeric Gq-protein
Components
  • Complex: A61603-bound alpha-1A-adrenergic receptor in complex with heterotrimeric Gq-protein
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(q) 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: Single fab chain (scFv16)
    • Protein or peptide: Endolysin,Alpha-1A adrenergic receptor
  • Ligand: N-[(5S)-5-(4,5-dihydro-1H-imidazol-2-yl)-2-hydroxy-5,6,7,8-tetrahydronaphthalen-1-yl]methanesulfonamide

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Supramolecule #1: A61603-bound alpha-1A-adrenergic receptor in complex with heterot...

SupramoleculeName: A61603-bound alpha-1A-adrenergic receptor in complex with heterotrimeric Gq-protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine n...

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(q) subunit alpha
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.084832 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSTVSAEDK AAAERSKMID KNLREDGEKA RRTLRLLLLG ADNSGKSTIV KQMRILHGGS GGSGGTSGIF ETKFQVDKVN FHMFDVGGQ RDERRKWIQC FNDVTAIIFV VDSSDYNRLQ EALNDFKSIW NNRWLRTISV ILFLNKQDLL AEKVLAGKSK I EDYFPEFA ...String:
MGSTVSAEDK AAAERSKMID KNLREDGEKA RRTLRLLLLG ADNSGKSTIV KQMRILHGGS GGSGGTSGIF ETKFQVDKVN FHMFDVGGQ RDERRKWIQC FNDVTAIIFV VDSSDYNRLQ EALNDFKSIW NNRWLRTISV ILFLNKQDLL AEKVLAGKSK I EDYFPEFA RYTTPEDATP EPGEDPRVTR AKYFIRKEFV DISTASGDGR HICYPHFTCA VDTENARRIF NDCKDIILQM NL REYNLV

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-2, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(q) 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: Homo sapiens (human)
Molecular weightTheoretical: 39.418086 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 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 frugiperda (fall armyworm)
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: Single fab chain (scFv16)

MacromoleculeName: Single fab chain (scFv16) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.668922 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KAAALEVLFQ GPHHHHHHHH

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Macromolecule #5: Endolysin,Alpha-1A adrenergic receptor

MacromoleculeName: Endolysin,Alpha-1A adrenergic receptor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: lysozyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.485246 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKNIFEML RIDEGLRLKI YKDTEGYYTI GIGHLLTKSP SLNAAKSELD KAIGRNTNGV ITKDEAEKL FNQDVDAAVR GILRNAKLKP VYDSLDAVRR AALINMVFQM GETGVAGFTN SLRMLQQKRW DEAAVNLAKS R WYNQTPNR ...String:
MKTIIALSYI FCLVFADYKD DDDKNIFEML RIDEGLRLKI YKDTEGYYTI GIGHLLTKSP SLNAAKSELD KAIGRNTNGV ITKDEAEKL FNQDVDAAVR GILRNAKLKP VYDSLDAVRR AALINMVFQM GETGVAGFTN SLRMLQQKRW DEAAVNLAKS R WYNQTPNR AKRVITTFRT GTWDAYAAAT QPPAPVNISK AILLGVILGG LILFGVLGNI LVILSVACHR HLHSVTHYYI VN LAVADLL LTSTVLPFSA IFEVLGYWAF GRVFCNIWAA VDVLCCTASI MGLCIISIDR YIGVSYPLRY PTIVTQRRGL MAL LCVWAL SLVISIGPLF GWRQPAPEDE TICQINEEPG YVLFSALGSF YLPLAIILVM YCRVYVVAKR ESRGLKSGLK TDKS HFSVR LLKFSREKKA AKTLGIVVGC FVLCWLPFFL VMPIGSFFPD FKPSETVFKI VFWLGYLNSC INPIIYPCSS QEFKK AFQN VLRIQCLCRK QASLEVLFQ

UniProtKB: Endolysin, Alpha-1A adrenergic receptor

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Macromolecule #6: N-[(5S)-5-(4,5-dihydro-1H-imidazol-2-yl)-2-hydroxy-5,6,7,8-tetrah...

MacromoleculeName: N-[(5S)-5-(4,5-dihydro-1H-imidazol-2-yl)-2-hydroxy-5,6,7,8-tetrahydronaphthalen-1-yl]methanesulfonamide
type: ligand / ID: 6 / Number of copies: 1 / Formula: CGZ
Molecular weightTheoretical: 309.384 Da
Chemical component information

ChemComp-CGZ:
N-[(5S)-5-(4,5-dihydro-1H-imidazol-2-yl)-2-hydroxy-5,6,7,8-tetrahydronaphthalen-1-yl]methanesulfonamide

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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

Concentration2.5 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6wha

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 360489
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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