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- PDB-9w3f: Cryo-EM structure of the human beta2-adrenergic receptor in compl... -

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Basic information

Entry
Database: PDB / ID: 9w3f
TitleCryo-EM structure of the human beta2-adrenergic receptor in complex with a novel antagonist
Components
  • Beta-2 adrenergic receptor,Endolysin
  • Beta2 adrenogic receptor inactive-state stabling nanobody Nb60
KeywordsMEMBRANE PROTEIN / Antagonist / GPCR
Function / homology
Function and homology information


beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / AMPA selective glutamate receptor signaling pathway / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / positive regulation of autophagosome maturation / heat generation / norepinephrine binding / Adrenoceptors / negative regulation of smooth muscle contraction ...beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / AMPA selective glutamate receptor signaling pathway / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / positive regulation of autophagosome maturation / heat generation / norepinephrine binding / Adrenoceptors / negative regulation of smooth muscle contraction / positive regulation of cardiac muscle cell contraction / positive regulation of lipophagy / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / adrenergic receptor signaling pathway / response to psychosocial stress / diet induced thermogenesis / endosome to lysosome transport / positive regulation of cAMP/PKA signal transduction / smooth muscle contraction / negative regulation of cardiac muscle cell apoptotic process / adenylate cyclase binding / potassium channel regulator activity / bone resorption / positive regulation of bone mineralization / viral release from host cell by cytolysis / neuronal dense core vesicle / intercellular bridge / regulation of sodium ion transport / adenylate cyclase-activating adrenergic receptor signaling pathway / peptidoglycan catabolic process / positive regulation of cardiac muscle cell apoptotic process / receptor-mediated endocytosis / brown fat cell differentiation / response to cold / clathrin-coated endocytic vesicle membrane / cellular response to amyloid-beta / cell wall macromolecule catabolic process / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / lysozyme / lysozyme activity / mitotic spindle / Cargo recognition for clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / Clathrin-mediated endocytosis / microtubule cytoskeleton / transcription by RNA polymerase II / G alpha (s) signalling events / host cell cytoplasm / early endosome / positive regulation of MAPK cascade / cell surface receptor signaling pathway / lysosome / signaling receptor complex / defense response to bacterium / endosome / endosome membrane / apical plasma membrane / Ub-specific processing proteases / cilium / ciliary basal body / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme-like domain superfamily ...Beta 2 adrenoceptor / Adrenoceptor family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme-like domain superfamily / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
BERBERINE / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsXu, T. / Liu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2026
Title: A negative survival pressure selection system enables GPCR antagonist screening.
Authors: Tao Xu / Qinxin Sun / Shuhao Zhang / Tingzhu Liu / Xiaoou Sun / Xusheng Wang / Bin Lin / Zhongjie Liu / Juan Wang / Guodong He / Xiangyu Liu /
History
DepositionJul 29, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Beta-2 adrenergic receptor,Endolysin
B: Beta2 adrenogic receptor inactive-state stabling nanobody Nb60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4003
Polymers72,0642
Non-polymers3361
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Beta-2 adrenergic receptor,Endolysin / Beta-2 adrenoreceptor / Beta-2 adrenoceptor / Lysis protein / Lysozyme / Muramidase


Mass: 58532.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: ADRB2, ADRB2R, B2AR, E / Production host: Spodoptera (butterflies/moths) / References: UniProt: P07550, UniProt: P00720, lysozyme
#2: Protein Beta2 adrenogic receptor inactive-state stabling nanobody Nb60


Mass: 13531.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Chemical ChemComp-BER / BERBERINE


Mass: 336.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Cryo-EM structure of the human beta2-adereneegic receptor in complex with a novel antagonist
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera (butterflies/moths)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 347166 / Symmetry type: POINT
RefinementHighest resolution: 3.04 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033066
ELECTRON MICROSCOPYf_angle_d0.4254185
ELECTRON MICROSCOPYf_dihedral_angle_d5.563426
ELECTRON MICROSCOPYf_chiral_restr0.038497
ELECTRON MICROSCOPYf_plane_restr0.003506

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