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- EMDB-19683: Cryo-EM structure of cell-free synthesized Human beta-1 adrenergi... -

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Basic information

Entry
Database: EMDB / ID: EMD-19683
TitleCryo-EM structure of cell-free synthesized Human beta-1 adrenergic receptor cotranslationally inserted into a lipidic nanodiscs
Map data
Sample
  • Complex: Complex between, human Beta-1 adrenergic receptor, Gs, and nanobody-35
    • Complex: Heterotrimeric Gs complex
      • Protein or peptide: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
      • 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
    • Complex: Beta-1 adrenergic receptor
      • Protein or peptide: Beta-1 adrenergic receptor
    • Complex: Nanobody-35
      • Protein or peptide: Nanobody-35
  • Ligand: ISOPRENALINE
KeywordsSignal transduction / GPCR / co-translational nanodisc insertion / G-protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of heart rate by epinephrine-norepinephrine / positive regulation of the force of heart contraction by epinephrine-norepinephrine / beta-adrenergic receptor activity / beta1-adrenergic receptor activity / G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / alpha-2A adrenergic receptor binding / regulation of circadian sleep/wake cycle, sleep / fear response / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation ...positive regulation of heart rate by epinephrine-norepinephrine / positive regulation of the force of heart contraction by epinephrine-norepinephrine / beta-adrenergic receptor activity / beta1-adrenergic receptor activity / G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / alpha-2A adrenergic receptor binding / regulation of circadian sleep/wake cycle, sleep / fear response / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / Adrenoceptors / negative regulation of multicellular organism growth / diet induced thermogenesis / neuronal dense core vesicle / PKA activation in glucagon signalling / hair follicle placode formation / developmental growth / D1 dopamine receptor binding / intracellular transport / vascular endothelial cell response to laminar fluid shear stress / brown fat cell differentiation / renal water homeostasis / Hedgehog 'off' state / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / regulation of insulin secretion / cellular response to glucagon stimulus / adenylate cyclase activator activity / response to cold / trans-Golgi network membrane / PDZ domain binding / negative regulation of inflammatory response to antigenic stimulus / Schaffer collateral - CA1 synapse / bone development / G-protein beta/gamma-subunit complex binding / platelet aggregation / Olfactory Signaling Pathway / cognition / 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 / adenylate cyclase-activating G protein-coupled 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 / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / 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 / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / ADP signalling through P2Y purinoceptor 1 / 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 / sensory perception of smell / 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) / positive regulation of cold-induced thermogenesis / G protein activity / GTPase binding / Ca2+ pathway / retina development in camera-type eye / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / fibroblast proliferation / G alpha (i) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / Ras protein signal transduction / early endosome / Extra-nuclear estrogen signaling / cell population proliferation / positive regulation of MAPK cascade / G protein-coupled receptor signaling pathway / protein heterodimerization activity / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding
Similarity search - Function
Beta 1 adrenoceptor / Adrenoceptor family / G-protein alpha subunit, group S / 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 ...Beta 1 adrenoceptor / Adrenoceptor family / G-protein alpha subunit, group S / 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) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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
Beta-1 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(s) subunit alpha isoforms short
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMerino F / Koeck Z / Ermel U / Dahlhaus P / Doetsch V / Kubicek J / Frangakis AS / Hilger D / Bernhard F
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)BE1911/9-1 Germany
German Research Foundation (DFG)FR 1653/12-2 Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of cell-free synthesized Human beta-1 adrenergic receptor cotranslationally inserted into a lipidic nanodiscs
Authors: Merino F / Koeck Z / Ermel U / Dahlhaus P / Doetsch V / Frangakis AS / Hilger D / Bernhard F
History
DepositionFeb 19, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19683.png

Downloads & links

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Map

FileDownload / File: emd_19683.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 300 pix.
= 339.906 Å		1.13 Å/pix.
x 300 pix.
= 339.906 Å		1.13 Å/pix.
x 300 pix.
= 339.906 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13302 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.03213412 - 0.072756305
Average (Standard dev.)-0.00012307832 (±0.0013349793)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 339.906 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19683_msk_1.map
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Mask #2

Fileemd_19683_msk_2.map
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Additional map: #2

Fileemd_19683_additional_1.map
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Additional map: #1

Fileemd_19683_additional_2.map
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Half map: #2

Fileemd_19683_half_map_1.map
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Half map: #1

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Sample components

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Entire : Complex between, human Beta-1 adrenergic receptor, Gs, and nanobody-35

EntireName: Complex between, human Beta-1 adrenergic receptor, Gs, and nanobody-35
Components
  • Complex: Complex between, human Beta-1 adrenergic receptor, Gs, and nanobody-35
    • Complex: Heterotrimeric Gs complex
      • Protein or peptide: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
      • 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
    • Complex: Beta-1 adrenergic receptor
      • Protein or peptide: Beta-1 adrenergic receptor
    • Complex: Nanobody-35
      • Protein or peptide: Nanobody-35
  • Ligand: ISOPRENALINE

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Supramolecule #1: Complex between, human Beta-1 adrenergic receptor, Gs, and nanobody-35

SupramoleculeName: Complex between, human Beta-1 adrenergic receptor, Gs, and nanobody-35
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3, #5, #4
Details: The GPCR was produced cell-free and co-translationally inserted into a lipidic nanodisc. Additional Gs and Nanobody-35 during GPCR production leads to the full assembly of the complex.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15 KDa

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Supramolecule #2: Heterotrimeric Gs complex

SupramoleculeName: Heterotrimeric Gs complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Details: Produced in T. ni cells for later in vitro assembly of full complex.
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Beta-1 adrenergic receptor

SupramoleculeName: Beta-1 adrenergic receptor / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Details: cell-free synthesized gpcr co-translationally inserted into a nanodisc
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Nanobody-35

SupramoleculeName: Nanobody-35 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4 / Details: Nanobody that binds to Galpha-Gbeta
Source (natural)Organism: Lama glama (llama)

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Macromolecule #1: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit...

MacromoleculeName: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.32616 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG DSEKATKVQD IKNNLKEAI ETIVAAMSNL VPPVELANPE NQFRVDYILS VMNVPDFDFP PEFYEHAKAL WEDEGVRACY ERSNEYQLID C AQYFLDKI ...String:
MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG DSEKATKVQD IKNNLKEAI ETIVAAMSNL VPPVELANPE NQFRVDYILS VMNVPDFDFP PEFYEHAKAL WEDEGVRACY ERSNEYQLID C AQYFLDKI DVIKQADYVP SDQDLLRCRV LTSGIFETKF QVDKVNFHMF DVGGQRDERR KWIQCFNDVT AIIFVVASSS YN MVIREDN QTNRLQEALN LFKSIWNNRW LRTISVILFL NKQDLLAEKV LAGKSKIEDY FPEFARYTTP EDATPEPGED PRV TRAKYF IRDEFLRIST ASGDGRHYCY PHFTCAVDTE NIRRVFNDCR DIIQRMHLRQ YELL

UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

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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: 37.728152 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD ...String:
GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD TTCALWDIET GQQTTTFTGH TGDVMSLSLA PDTRLFVSGA CDASAKLWDV REGMCRQTFT GHESDINAIC FF PNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRAGVLAGHD NRV SCLGVT DDGMAVATGS WDSFLKIWN

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: 7.56375 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFC

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

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Macromolecule #4: Nanobody-35

MacromoleculeName: Nanobody-35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 14.71432 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQPGGSLRL SCAASGFTFS NYKMNWVRQA PGKGLEWVSD ISQSGASISY TGSVKGRFTI SRDNAKNTLY LQMNSLKPE DTAVYYCARC PAPFTRDCFD VTSTTYAYRG QGTQVTVSSH HHHHH

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Macromolecule #5: Beta-1 adrenergic receptor

MacromoleculeName: Beta-1 adrenergic receptor / type: protein_or_peptide / ID: 5 / Details: Cell-free synthesized / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.130328 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGAGVLVLGA SEPGNLSSAA PLPDGAATAA RLLVPASPPA SLLPPASESP EPLSQQWTAG MGLLMALIVL LIVAGNVLVI VAIASTPRL QTLTNLFIMS LASADLVVGL LVVPFGATIV VWGRWEYGSF FCELWTSVDV LCVTASVWTL CVIALDRYLA I TSPFRYQS ...String:
MGAGVLVLGA SEPGNLSSAA PLPDGAATAA RLLVPASPPA SLLPPASESP EPLSQQWTAG MGLLMALIVL LIVAGNVLVI VAIASTPRL QTLTNLFIMS LASADLVVGL LVVPFGATIV VWGRWEYGSF FCELWTSVDV LCVTASVWTL CVIALDRYLA I TSPFRYQS LLTRARARGL VCTVWAISAL VSFLPILMHW WRAESDEARR CYNDPKCCDF VTNRAYAIAS SVVSFYVPLC IM AFVYLRV FREAQKQVKK IDSCERRFLG GPARPPSPSP SPVPAPAPPP GPPRPAAAAA TAPLANGRAG KRRPSRLVLL REQ KALKTL GIIMGVFTLC WLPFFLANVV KAFHRELVPD RLFVAFNWLG YANSAMNPII YCRSPDFRKA FQGLLAAARR AARR RHATH GDRPRASGCL ARPGPPPSPG AASDDDDDDV VGATPPARLL EPWAGCNGGA AADSDSSLDE PCRPGFASES KV

UniProtKB: Beta-1 adrenergic receptor

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Macromolecule #6: ISOPRENALINE

MacromoleculeName: ISOPRENALINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: 5FW
Molecular weightTheoretical: 211.258 Da
Chemical component information

ChemComp-5FW:
ISOPRENALINE / medication*YM

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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

Concentration0.7 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 9.0 sec. / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 235380
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Model from a previous processing of the data. Initial model was generated using SGD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 74266
Initial angle assignmentType: OTHER / Software - Name: RELION
Final angle assignmentType: OTHER / Software - Name: RELION
Final 3D classificationNumber classes: 3 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

6e3y

source_name: PDB, initial_model_type: experimental modelUsed for Gs and Nb35
source_name: AlphaFold, initial_model_type: in silico modelUSed for beta-1 AR
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8s2t:
Cryo-EM structure of cell-free synthesized Human beta-1 adrenergic receptor cotranslationally inserted into a lipidic nanodiscs

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