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- EMDB-30681: Cryo-EM structure of the partial agonist salbutamol-bound beta2 a... -

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Entry
Database: EMDB / ID: EMD-30681
TitleCryo-EM structure of the partial agonist salbutamol-bound beta2 adrenergic receptor-Gs protein complex.
Map dataCryo-EM structure of the partial agonist salbutamol-bound beta2 adrenergic receptor-Gs complex.
Sample
  • Complex: Cryo-EM structure of the partial agonist salbutamol-bound beta2 adrenergic receptor-Gs protein complex.
    • Protein or peptide: 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
    • Protein or peptide: Nb35 nanobody
    • Protein or peptide: Beta-2 adrenergic receptor
  • Ligand: SALBUTAMOL
  • Ligand: water
Function / homology
Function and homology information


Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Activation of the phototransduction cascade / desensitization of G protein-coupled receptor signaling pathway by arrestin / beta2-adrenergic receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of mini excitatory postsynaptic potential / Activation of G protein gated Potassium channels / G-protein activation ...Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Activation of the phototransduction cascade / desensitization of G protein-coupled receptor signaling pathway by arrestin / beta2-adrenergic receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of mini excitatory postsynaptic potential / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / positive regulation of cAMP-dependent protein kinase activity / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / norepinephrine binding / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of AMPA receptor activity / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / activation of transmembrane receptor protein tyrosine kinase activity / G alpha (s) signalling events / negative regulation of smooth muscle contraction / G alpha (q) signalling events / positive regulation of lipophagy / response to psychosocial stress / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / negative regulation of multicellular organism growth / Vasopressin regulates renal water homeostasis via Aquaporins / endosome to lysosome transport / adrenergic receptor signaling pathway / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of protein kinase A signaling / PKA activation in glucagon signalling / hair follicle placode formation / adenylate cyclase binding / intracellular transport / D1 dopamine receptor binding / smooth muscle contraction / developmental growth / potassium channel regulator activity / Hedgehog 'off' state / positive regulation of bone mineralization / positive regulation of cAMP-mediated signaling / adenylate cyclase-activating adrenergic receptor signaling pathway / brown fat cell differentiation / regulation of sodium ion transport / bone resorption / activation of adenylate cyclase activity / receptor-mediated endocytosis / adenylate cyclase activator activity / response to cold / trans-Golgi network membrane / clathrin-coated endocytic vesicle membrane / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / bone development / positive regulation of protein serine/threonine kinase activity / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / photoreceptor disc membrane / platelet aggregation / Glucagon-type ligand receptors / cognition / Vasopressin regulates renal water homeostasis via Aquaporins / positive regulation of GTPase activity / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / sensory perception of taste / GPER1 signaling / cellular response to amyloid-beta / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / sensory perception of smell / Cargo recognition for clathrin-mediated endocytosis / retina development in camera-type eye / GTPase binding / Clathrin-mediated endocytosis
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / G-protein alpha subunit, group S / Serpentine type 7TM GPCR chemoreceptor Srsx / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit ...Beta 2 adrenoceptor / Adrenoceptor family / G-protein alpha subunit, group S / Serpentine type 7TM GPCR chemoreceptor Srsx / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / 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 / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Beta-2 adrenergic receptor / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Bos taurus (cattle) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsYang F / Ling SL / Zhou YX / Zhang YN / Lv P / Liu SL / Fang W / Sun WJ / Hu LYA
CitationJournal: Natl Sci Rev / Year: 2020
Title: Different Conformational Responses of the beta2-Adrenergic Receptor-Gs Complex upon Binding of the Partial Agonist Salbutamol or the Full Agonist Isoprenaline
Authors: Yang F / Ling SL / Zhou YX / Zhang YN / Lv P / Liu SL / Fang W / Sun WJ / Hu LYA / Zhang L / Shi P / Tian C
History
DepositionNov 15, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateDec 16, 2020-
Current statusDec 16, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dhi
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30681.png

Downloads & links

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Map

FileDownload / File: emd_30681.map.gz / Format: CCP4 / Size: 23.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the partial agonist salbutamol-bound beta2 adrenergic receptor-Gs complex.
Voxel sizeX=Y=Z: 1.014 Å
Density
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.09986864 - 0.16228904
Average (Standard dev.)0.0003053411 (±0.0050405846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions184184184
Spacing184184184
CellA=B=C: 186.576 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z184184184
origin x/y/z0.0000.0000.000
length x/y/z186.576186.576186.576
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS184184184
D min/max/mean-0.1000.1620.000

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of the partial agonist salbutamol-bound beta2 a...

EntireName: Cryo-EM structure of the partial agonist salbutamol-bound beta2 adrenergic receptor-Gs protein complex.
Components
  • Complex: Cryo-EM structure of the partial agonist salbutamol-bound beta2 adrenergic receptor-Gs protein complex.
    • Protein or peptide: 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
    • Protein or peptide: Nb35 nanobody
    • Protein or peptide: Beta-2 adrenergic receptor
  • Ligand: SALBUTAMOL
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of the partial agonist salbutamol-bound beta2 a...

SupramoleculeName: Cryo-EM structure of the partial agonist salbutamol-bound beta2 adrenergic receptor-Gs protein complex.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightExperimental: 151.4 kDa/nm

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Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

MacromoleculeName: 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: 45.812594 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SMGCLGNSKT EDQRNEEKAQ REANKKIEKQ LQKDKQVYRA THRLLLLGAG ESGKSTIVKQ MRILHVNGFN GEGGEEDPQA ARSNSDGEK ATKVQDIKNN LKEAIETIVA AMSNLVPPVE LANPENQFRV DYILSVMNVP DFDFPPEFYE HAKALWEDEG V RACYERSN ...String:
SMGCLGNSKT EDQRNEEKAQ REANKKIEKQ LQKDKQVYRA THRLLLLGAG ESGKSTIVKQ MRILHVNGFN GEGGEEDPQA ARSNSDGEK ATKVQDIKNN LKEAIETIVA AMSNLVPPVE LANPENQFRV DYILSVMNVP DFDFPPEFYE HAKALWEDEG V RACYERSN EYQLIDCAQY FLDKIDVIKQ ADYVPSDQDL LRCRVLTSGI FETKFQVDKV NFHMFDVGGQ RDERRKWIQC FN DVTAIIF VVASSSYNMV IREDNQTNRL QEALNLFKSI WNNRWLRTIS VILFLNKQDL LAEKVLAGKS KIEDYFPEFA RYT TPEDAT PEPGEDPRVT RAKYFIRDEF LRISTASGDG RHYCYPHFTC AVDTENIRRV FNDCRDIIQR MHLRQYELL

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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: Bos taurus (cattle)
Molecular weightTheoretical: 37.41693 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String:
MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN

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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: Bos taurus (cattle)
Molecular weightTheoretical: 8.805155 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHMAS NNTASIAQAR KLVEQLKMEA NIDRIKVSKA AADLMAYCEA HAKEDPLLTP VPASENPFRE KKFFSAIL

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Macromolecule #4: Nb35 nanobody

MacromoleculeName: Nb35 nanobody / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 17.057271 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKYLLPTAAA GLLLLAAQPA MAMQVQLQES GGGLVQPGGS LRLSCAASGF TFSNYKMNWV RQAPGKGLEW VSDISQSGAS ISYTGSVKG RFTISRDNAK NTLYLQMNSL KPEDTAVYYC ARCPAPFTRD CFDVTSTTYA YRGQGTQVTV SSHHHHHH

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Macromolecule #5: Beta-2 adrenergic receptor

MacromoleculeName: Beta-2 adrenergic receptor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.042906 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FSLVFADYKD DDDAMGQPGN GSAFLLAPNR SHAPDHDVTQ QRDEVWVVGM GIVMSLIVLA IVFGNVLVIT AIAKFERLQ TVTNYFITSL AVADLVMGLA VVPFGAAHIL TKTWTFGNFW CEFWTSIDVL CVTASIWTLV VIAVDRYFAI T SPFKYQSL ...String:
MKTIIALSYI FSLVFADYKD DDDAMGQPGN GSAFLLAPNR SHAPDHDVTQ QRDEVWVVGM GIVMSLIVLA IVFGNVLVIT AIAKFERLQ TVTNYFITSL AVADLVMGLA VVPFGAAHIL TKTWTFGNFW CEFWTSIDVL CVTASIWTLV VIAVDRYFAI T SPFKYQSL LTKNKARVII LMVWIVSGLT SFLPIQMHWY RATHQEAINC YAEETCCDFF TNQAYAIASS IVSFYVPLVI MV FVYSRVF QEAKRQLQKI DKSEGRFHVQ NRSSKFALKE HKALKTLGII MGTFTLAWLP FFIVNIVHVI QDNLIRKEVY ILL NWIGYV NSGFNPLIYS RSPDFRIAFQ ELLCLRRSSL KHHHHHHHHH H

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Macromolecule #6: SALBUTAMOL

MacromoleculeName: SALBUTAMOL / type: ligand / ID: 6 / Number of copies: 1 / Formula: 68H
Molecular weightTheoretical: 239.311 Da
Chemical component information

ChemComp-68H:
SALBUTAMOL / medication, agonist*YM / Salbutamol

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

BufferpH: 7.5
GridModel: Quantifoil / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 57.6 e/Å2
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:

7bz2

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 455803

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