9RX1 | pdb_00009rx1

Cryo-EM structure of a single-chain beta1-adrenoceptor - AmpC beta-lactamase fusion protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Cryo-EM structure of a single-chain beta 1-adrenoceptor - AmpC beta-lactamase fusion protein.

Collu, G.Mohammed, I.Lafita, A.Bierig, T.Poghosyan, E.Bliven, S.Rabl, J.Afanasyev, P.Benoit, R.M.

(2026) J Struct Biol : 108349-108349

  • DOI: https://doi.org/10.1016/j.jsb.2026.108349
  • Primary Citation Related Structures: 
    9RX1

  • PubMed Abstract: 

    The insertion of fusion proteins has enabled the crystallization of a wide range of G-protein-coupled receptors. Here, we adapted this engineering strategy to cryo-electron microscopy (cryo-EM). We inserted the soluble protein AmpC β-lactamase into the third intracellular loop (ICL3) of ultra-thermostable β1-adrenoceptor (β1AR) via chimeric helix fusions. Biochemical and biophysical characterization showed that the resulting fusion protein after expression, solubilization and purification was monodisperse and able to bind the known β1AR weak partial agonist cyanopindolol, and the antagonist propranolol. The protein particles comprised sufficient mass and discernable structural features to elucidate its cryo-EM structure in complex with cyanopindolol without any natural (G-proteins, arrestins) or artificial (Nanobodies, DARPins) binding partners, to an overall resolution of 4.2 Å. The seven-helix architecture and helix eight, as well as both GPCR - AmpC β-lactamase connections are clearly resolved. β1AR is in an inactive-like conformation. 3D variability analysis revealed significant flexibility between the two protein domains and within the GPCR helices. The map contains clear density for the cyanopindolol. The fusion protein geometry is expected to be compatible with a subset of other class A GPCRs exhibiting suitable architecture. For receptors meeting these geometric requirements, this approach may facilitate cryo-EM structure determination of GPCR-ligand complexes in an inactive-like state. In addition, it could support structural studies of GPCRs in the absence of ligands.


  • Organizational Affiliation
    • Laboratory for Multiscale Bioimaging, PSI Center for Life Sciences, 5232 Villigen PSI, Switzerland; Department of Biology, ETH Zurich, 8093 Zurich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 73.27 kDa 
  • Atom Count: 4,972 
  • Modeled Residue Count: 629 
  • Deposited Residue Count: 654 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-1 adrenergic receptor,Beta-lactamase654Meleagris gallopavoEscherichia coli K-12Mutation(s): 11 
Gene Names: ADRB1ampCampAb4150JW4111
EC: 3.5.2.6
UniProt
Find proteins for P00811 (Escherichia coli (strain K12))
Explore P00811 
Go to UniProtKB:  P00811
Find proteins for P07700 (Meleagris gallopavo)
Explore P07700 
Go to UniProtKB:  P07700
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP07700P00811
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P32
(Subject of Investigation/LOI)

Query on P32



Download:Ideal Coordinates CCD File
B [auth A]Cyanopindolol
C16 H21 N3 O2
CQEFAUFOQSCRMZ-LBPRGKRZSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novartis FreeNovation--
Promedica SiftungSwitzerland1401/M
Swiss National Science FoundationSwitzerlandCRSK-3_190414

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-22
    Type: Initial release
  • Version 1.1: 2026-07-29
    Changes: Data collection, Database references