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- EMDB-4390: Cryo-EM structure of the adenosine A2A receptor bound to a miniGs... -

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Basic information

Entry
Database: EMDB / ID: EMD-4390
TitleCryo-EM structure of the adenosine A2A receptor bound to a miniGs heterotrimer
Map data
Sample
  • Complex: Adenosine A2A receptor bound to miniGs heterotrimer
    • Complex: Adenosine receptor A2aAdenosine A2A receptor
      • Protein or peptide: TrxA,Adenosine receptor A2a
    • Complex: miniGs heterotrimer
      • 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: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Complex: nanobody Nb35
      • Protein or peptide: nanobody Nb35
  • Ligand: N-ETHYL-5'-CARBOXAMIDO ADENOSINE
Function / homology
Function and homology information


positive regulation of acetylcholine secretion, neurotransmission / regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / negative regulation of alpha-beta T cell activation / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / positive regulation of urine volume ...positive regulation of acetylcholine secretion, neurotransmission / regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / negative regulation of alpha-beta T cell activation / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / positive regulation of urine volume / NGF-independant TRKA activation / Surfactant metabolism / protein kinase C-activating G protein-coupled receptor signaling pathway / synaptic transmission, dopaminergic / synaptic transmission, cholinergic / inhibitory postsynaptic potential / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / intermediate filament / response to caffeine / eating behavior / DNA polymerase processivity factor activity / presynaptic active zone / alpha-actinin binding / membrane depolarization / PKA activation in glucagon signalling / regulation of calcium ion transport / hair follicle placode formation / intracellular transport / asymmetric synapse / axolemma / D1 dopamine receptor binding / protein-disulfide reductase activity / developmental growth / response to inorganic substance / Hedgehog 'off' state / cellular defense response / positive regulation of cAMP-mediated signaling / prepulse inhibition / phagocytosis / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of apoptotic signaling pathway / response to amphetamine / excitatory postsynaptic potential / activation of adenylate cyclase activity / adenylate cyclase activator activity / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / cell redox homeostasis / neuron projection morphogenesis / regulation of mitochondrial membrane potential / trans-Golgi network membrane / locomotory behavior / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / apoptotic signaling pathway / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / bone development / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / 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 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / platelet aggregation / cognition / negative regulation of inflammatory response / Glucagon-type ligand receptors / 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 / vasodilation / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / Thioredoxin / Thioredoxin / G-protein alpha subunit, group S / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Serpentine type 7TM GPCR chemoreceptor Srsx ...Adenosine A2A receptor / Adenosine receptor / Thioredoxin / Thioredoxin / G-protein alpha subunit, group S / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / 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) / Thioredoxin-like superfamily / 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
Thioredoxin 1 / Adenosine receptor A2a / 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 / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Homo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.11 Å
AuthorsGarcia-Nafria J / Lee Y
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
European Research CouncilEMPSI 339995 United Kingdom
Medical Research Council (United Kingdom)MRC U105197215 United Kingdom
CitationJournal: Elife / Year: 2018
Title: Cryo-EM structure of the adenosine A receptor coupled to an engineered heterotrimeric G protein.
Authors: Javier García-Nafría / Yang Lee / Xiaochen Bai / Byron Carpenter / Christopher G Tate /
Abstract: The adenosine A receptor (AR) is a prototypical G protein-coupled receptor (GPCR) that couples to the heterotrimeric G protein G. Here, we determine the structure by electron cryo-microscopy (cryo-EM) ...The adenosine A receptor (AR) is a prototypical G protein-coupled receptor (GPCR) that couples to the heterotrimeric G protein G. Here, we determine the structure by electron cryo-microscopy (cryo-EM) of AR at pH 7.5 bound to the small molecule agonist NECA and coupled to an engineered heterotrimeric G protein, which contains mini-G, the βγ subunits and nanobody Nb35. Most regions of the complex have a resolution of ~3.8 Å or better. Comparison with the 3.4 Å resolution crystal structure shows that the receptor and mini-G are virtually identical and that the density of the side chains and ligand are of comparable quality. However, the cryo-EM density map also indicates regions that are flexible in comparison to the crystal structures, which unexpectedly includes regions in the ligand binding pocket. In addition, an interaction between intracellular loop 1 of the receptor and the β subunit of the G protein was observed.
History
DepositionApr 23, 2018-
Header (metadata) releaseMay 16, 2018-
Map releaseMay 16, 2018-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0631
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0631
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6gdg
  • Surface level: 0.0631
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4390.png

Downloads & links

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Map

FileDownload / File: emd_4390.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.0631 / Movie #1: 0.0631
Minimum - Maximum-0.17760025 - 0.29012117
Average (Standard dev.)0.0013410164 (±0.012475579)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 160.50002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z160.500160.500160.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.1780.2900.001

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Supplemental data

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Sample components

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Entire : Adenosine A2A receptor bound to miniGs heterotrimer

EntireName: Adenosine A2A receptor bound to miniGs heterotrimer
Components
  • Complex: Adenosine A2A receptor bound to miniGs heterotrimer
    • Complex: Adenosine receptor A2aAdenosine A2A receptor
      • Protein or peptide: TrxA,Adenosine receptor A2a
    • Complex: miniGs heterotrimer
      • 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: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Complex: nanobody Nb35
      • Protein or peptide: nanobody Nb35
  • Ligand: N-ETHYL-5'-CARBOXAMIDO ADENOSINE

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Supramolecule #1: Adenosine A2A receptor bound to miniGs heterotrimer

SupramoleculeName: Adenosine A2A receptor bound to miniGs heterotrimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Molecular weightTheoretical: 137 KDa

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Supramolecule #2: Adenosine receptor A2a

SupramoleculeName: Adenosine receptor A2a / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #3: miniGs heterotrimer

SupramoleculeName: miniGs heterotrimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #4: nanobody Nb35

SupramoleculeName: nanobody Nb35 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Lama glama (llama)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: TrxA,Adenosine receptor A2a

MacromoleculeName: TrxA,Adenosine receptor A2a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.909785 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAAH HHHHHHHHHE NLYFQGSDKI IHLTDDSFDT DVLKADGAIL VDFWAEWSG PSKMIAPILD EIADEYQGKL TVAKLNIDQN PGTAPKYGIR GIPTLLLFAN GEVAATKVGA LSKGQLKEFL D ANLAEAAA ...String:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAAH HHHHHHHHHE NLYFQGSDKI IHLTDDSFDT DVLKADGAIL VDFWAEWSG PSKMIAPILD EIADEYQGKL TVAKLNIDQN PGTAPKYGIR GIPTLLLFAN GEVAATKVGA LSKGQLKEFL D ANLAEAAA KAVYITVELA IAVLAILGNV LVCWAVWLNS NLQNVTNYFV VSLAAADIAV GVLAIPFAIT ISTGFCAACH GC LFIACFV LVLTQSSIFS LLAIAIDRYI AIRIPLRYNG LVTGTRAKGI IAICWVLSFA IGLTPMLGWN NCGQPKEGKA HSQ GCGEGQ VACLFEDVVP MNYMVYFNFF ACVLVPLLLM LGVYLRIFLA ARRQLKQMES QPLPGERARS TLQKEVHAAK SLAI IVGLF ALCWLPLHII NCFTFFCPDC SHAPLWLMYL AIVLSHTNSV VNPFIYAYRI REFRQTFRKI IRSHVLRQQE PFKA

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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: 37.285734 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLII WDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR FLDDNQIVTS S GDTTCALW ...String:
SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLII WDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR FLDDNQIVTS S GDTTCALW DIETGQQTTT FTGHTGDVMS LSLAPDTRLF VSGACDASAK LWDVREGMCR QTFTGHESDI NAICFFPNGN AF ATGSDDA TCRLFDLRAD QELMTYSHDN IICGITSVSF SKSGRLLLAG YDDFNCNVWD ALKADRAGVL AGHDNRVSCL GVT DDGMAV 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: 7.845078 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFSAI L

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Macromolecule #4: Guanine nucleotide-binding protein G(s) subunit alpha isoforms sh...

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.907684 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: NSKTEDQRNE EKAQREANKK IEKQLQKDKQ VYRATHRLLL LGADNSGKST IVKQMRILHG GSGGSGGTSG IFETKFQVDK VNFHMFDVG GQRDERRKWI QCFNDVTAII FVVDSSDYNR LQEALNLFKS IWNNRWLRTI SVILFLNKQD LLAEKVLAGK S KIEDYFPE ...String:
NSKTEDQRNE EKAQREANKK IEKQLQKDKQ VYRATHRLLL LGADNSGKST IVKQMRILHG GSGGSGGTSG IFETKFQVDK VNFHMFDVG GQRDERRKWI QCFNDVTAII FVVDSSDYNR LQEALNLFKS IWNNRWLRTI SVILFLNKQD LLAEKVLAGK S KIEDYFPE FARYTTPEDA TPEPGEDPRV TRAKYFIRDE FLRISTASGD GRHYCYPHFT CAVDTENARR IFNDCRDIIQ RM HLRQYEL L

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Macromolecule #5: nanobody Nb35

MacromoleculeName: nanobody Nb35 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 16.926076 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKYLLPTAAA GLLLLAAQPA MAQVQLQESG GGLVQPGGSL RLSCAASGFT FSNYKMNWVR QAPGKGLEWV SDISQSGASI SYTGSVKGR FTISRDNAKN TLYLQMNSLK PEDTAVYYCA RCPAPFTRDC FDVTSTTYAY RGQGTQVTVS SHHHHHH

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Macromolecule #6: N-ETHYL-5'-CARBOXAMIDO ADENOSINE

MacromoleculeName: N-ETHYL-5'-CARBOXAMIDO ADENOSINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: NEC
Molecular weightTheoretical: 308.293 Da
Chemical component information

ChemComp-NEC:
N-ETHYL-5'-CARBOXAMIDO ADENOSINE

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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

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 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 opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 60.0 sec. / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. v0.1.06)
Startup modelType of model: OTHER / Details: ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 128002

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-6gdg:
Cryo-EM structure of the adenosine A2A receptor bound to a miniGs heterotrimer

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