[English] 日本語
Yorodumi
- PDB-6gdg: Cryo-EM structure of the adenosine A2A receptor bound to a miniGs... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gdg
TitleCryo-EM structure of the adenosine A2A receptor bound to a miniGs heterotrimer
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • TrxA,Adenosine receptor A2a
  • nanobody Nb35
KeywordsMEMBRANE PROTEIN / G-protein coupled receptor / adenosine / GPCR / A2A receptor
Function / homology
Function and homology information


regulation of norepinephrine secretion / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / Surfactant metabolism ...regulation of norepinephrine secretion / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / Surfactant metabolism / sensory perception / positive regulation of urine volume / synaptic transmission, dopaminergic / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / synaptic transmission, cholinergic / positive regulation of glutamate secretion / intermediate filament / presynaptic active zone / blood circulation / response to caffeine / eating behavior / inhibitory postsynaptic potential / DNA polymerase processivity factor activity / alpha-actinin binding / regulation of calcium ion transport / protein-disulfide reductase activity / asymmetric synapse / PKA activation in glucagon signalling / axolemma / developmental growth / membrane depolarization / hair follicle placode formation / phagocytosis / D1 dopamine receptor binding / cellular defense response / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / intracellular transport / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / activation of adenylate cyclase activity / Hedgehog 'off' state / adenylate cyclase-activating adrenergic receptor signaling pathway / neuron projection morphogenesis / cellular response to glucagon stimulus / astrocyte activation / presynaptic modulation of chemical synaptic transmission / regulation of insulin secretion / cell redox homeostasis / response to amphetamine / adenylate cyclase activator activity / central nervous system development / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / positive regulation of apoptotic signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of mitochondrial membrane potential / positive regulation of protein secretion / excitatory postsynaptic potential / synaptic transmission, glutamatergic / locomotory behavior / apoptotic signaling pathway / negative regulation of inflammatory response to antigenic stimulus / bone development / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / platelet aggregation / G-protein beta/gamma-subunit complex binding / vasodilation / cognition / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / blood coagulation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / sensory perception of smell / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / G-protein alpha subunit, group S / Thioredoxin domain profile. / Thioredoxin domain / Serpentine type 7TM GPCR chemoreceptor Srsx ...Adenosine A2A receptor / Adenosine receptor / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / G-protein alpha subunit, group S / Thioredoxin domain profile. / Thioredoxin domain / 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 / G protein beta WD-40 repeat protein / 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) / WD domain, G-beta repeat / Thioredoxin-like 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. / 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
N-ETHYL-5'-CARBOXAMIDO ADENOSINE / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.11 Å
AuthorsGarcia-Nafria, J. / Lee, Y.
Funding support United Kingdom, 2items
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, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4390
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TrxA,Adenosine receptor A2a
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
C: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
D: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
E: nanobody Nb35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,1836
Polymers143,8745
Non-polymers3081
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11250 Å2
ΔGint-67 kcal/mol
Surface area39720 Å2
MethodPISA

-
Components

-
Guanine nucleotide-binding protein ... , 3 types, 3 molecules BCD

#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37285.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62873
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7845.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P59768
#4: Protein Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Adenylate cyclase-stimulating G alpha protein


Mass: 28907.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAS, GNAS1, GSP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P63092

-
Protein / Antibody / Non-polymers , 3 types, 3 molecules AE

#1: Protein TrxA,Adenosine receptor A2a


Mass: 52909.785 Da / Num. of mol.: 1 / Fragment: UNP residues 37-144,UNP residues 8-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: trxA, ADORA2A, ADORA2 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q14F07, UniProt: P29274, UniProt: P0AA25*PLUS
#5: Antibody nanobody Nb35


Mass: 16926.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#6: Chemical ChemComp-NEC / N-ETHYL-5'-CARBOXAMIDO ADENOSINE


Mass: 308.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N6O4

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Adenosine A2A receptor bound to miniGs heterotrimerCOMPLEX#1-#50MULTIPLE SOURCES
2Adenosine receptor A2aCOMPLEX#11RECOMBINANT
3miniGs heterotrimerCOMPLEX#2-#41RECOMBINANT
4nanobody Nb35COMPLEX#51RECOMBINANT
Molecular weightValue: 0.137 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Trichoplusia ni (cabbage looper)7111
23Trichoplusia ni (cabbage looper)7111
34Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 60 sec. / Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
2EPUimage acquisition
4Gctfv0.1.06CTF correction
7Cootmodel fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION3D reconstruction
13REFMAC5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128002 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more