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- PDB-8ugw: Computational design of highly signaling active membrane receptor... -

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Basic information

Entry
Database: PDB / ID: 8ugw
TitleComputational design of highly signaling active membrane receptors through de novo solvent-mediated allosteric networks
ComponentsEndolysin,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / The adenosine a2a receptor
Function / homology
Function and homology information


regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / 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 / sensory perception ...regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / 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 / sensory perception / Surfactant metabolism / positive regulation of urine volume / synaptic transmission, dopaminergic / inhibitory postsynaptic potential / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / positive regulation of glutamate secretion / synaptic transmission, cholinergic / response to caffeine / blood circulation / intermediate filament / eating behavior / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / phagocytosis / prepulse inhibition / cellular defense response / viral release from host cell by cytolysis / presynaptic modulation of chemical synaptic transmission / peptidoglycan catabolic process / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / regulation of mitochondrial membrane potential / central nervous system development / positive regulation of apoptotic signaling pathway / positive regulation of long-term synaptic potentiation / excitatory postsynaptic potential / positive regulation of synaptic transmission, GABAergic / synaptic transmission, glutamatergic / positive regulation of protein secretion / locomotory behavior / astrocyte activation / apoptotic signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell wall macromolecule catabolic process / blood coagulation / vasodilation / lysozyme / lysozyme activity / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / negative regulation of neuron apoptotic process / postsynaptic membrane / host cell cytoplasm / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / defense response to bacterium / inflammatory response / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / lipid binding / dendrite / regulation of DNA-templated transcription / protein-containing complex binding / glutamatergic synapse / enzyme binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. ...Adenosine A2A receptor / Adenosine receptor / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / Lysozyme-like domain superfamily / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Chem-NGI / Endolysin / Adenosine receptor A2a
Similarity search - Component
Biological speciesTequatrovirus T4
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsWang, J. / Chen, K.Y. / Lai, J.K. / Russell, A.M. / Conners, K. / Rutter, M.E. / Condon, B. / Tung, F. / Kodandapani, L. / Chau, B. ...Wang, J. / Chen, K.Y. / Lai, J.K. / Russell, A.M. / Conners, K. / Rutter, M.E. / Condon, B. / Tung, F. / Kodandapani, L. / Chau, B. / Zhao, X. / Benach, J. / Baker, K. / Hembre, E.J. / Barth, P.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat.Chem. / Year: 2025
Title: Computational design of highly signalling-active membrane receptors through solvent-mediated allosteric networks.
Authors: Chen, K.M. / Lai, J.K. / Rudden, L.S.P. / Wang, J. / Russell, A.M. / Conners, K. / Rutter, M.E. / Condon, B. / Tung, F. / Kodandapani, L. / Chau, B. / Zhao, X. / Benach, J. / Baker, K. / Hembre, E.J. / Barth, P.
History
DepositionOct 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 12, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin,Adenosine receptor A2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1882
Polymers52,6891
Non-polymers5001
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.179, 73.668, 149.847
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endolysin,Adenosine receptor A2a


Mass: 52688.711 Da / Num. of mol.: 1 / Fragment: residues 2-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tequatrovirus T4, (gene. exp.) Homo sapiens (human)
Gene: ADORA2A, ADORA2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00720, UniProt: P29274, lysozyme
#2: Chemical ChemComp-NGI / 2-[P-(2-CARBOXYETHYL)PHENYLETHYL-AMINO]-5'-N-ETHYLCARBOXAMIDO ADENOSINE


Mass: 499.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29N7O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 7
Details: 100mM Hepes pH 7 + 27% PEG 300 + 50mM Sodium Potassium Tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 3.9→66 Å / Num. obs: 6413 / % possible obs: 99.3 % / Redundancy: 6.3 % / Rsym value: 0.129 / Net I/σ(I): 7.2
Reflection shellResolution: 3.9→4.11 Å / Num. unique obs: 914 / CC1/2: 0.617 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O79, 5IU4

2o79

5iu4


Resolution: 3.9→66 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.33 --
Rwork0.3 --
obs-6413 99.3 %
Displacement parametersBiso max: 345.3 Å2 / Biso mean: 117.3931 Å2 / Biso min: 56.85 Å2
Refinement stepCycle: LAST / Resolution: 3.9→66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 36 0 3057

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