6IBL

ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND AGONIST FORMOTEROL AND NANOBODY Nb80


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.277 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2CVClick on this verticalbar to view detailsBest fitted H98Click on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

Molecular basis of beta-arrestin coupling to formoterol-bound beta1-adrenoceptor.

Lee, Y.Warne, T.Nehme, R.Pandey, S.Dwivedi-Agnihotri, H.Chaturvedi, M.Edwards, P.C.Garcia-Nafria, J.Leslie, A.G.W.Shukla, A.K.Tate, C.G.

(2020) Nature 583: 862-866

  • DOI: https://doi.org/10.1038/s41586-020-2419-1
  • Primary Citation of Related Structures:  
    6IBL, 6TKO

  • PubMed Abstract: 

    The β 1 -adrenoceptor (β 1 AR) is a G-protein-coupled receptor (GPCR) that couples 1 to the heterotrimeric G protein G s . G-protein-mediated signalling is terminated by phosphorylation of the C terminus of the receptor by GPCR kinases (GRKs) and by coupling of β-arrestin 1 (βarr1, also known as arrestin 2), which displaces G s and induces signalling through the MAP kinase pathway 2 . The ability of synthetic agonists to induce signalling preferentially through either G proteins or arrestins-known as biased agonism 3 -is important in drug development, because the therapeutic effect may arise from only one signalling cascade, whereas the other pathway may mediate undesirable side effects 4 . To understand the molecular basis for arrestin coupling, here we determined the cryo-electron microscopy structure of the β 1 AR-βarr1 complex in lipid nanodiscs bound to the biased agonist formoterol 5 , and the crystal structure of formoterol-bound β 1 AR coupled to the G-protein-mimetic nanobody 6 Nb80. βarr1 couples to β 1 AR in a manner distinct to that 7 of G s coupling to β 2 AR-the finger loop of βarr1 occupies a narrower cleft on the intracellular surface, and is closer to transmembrane helix H7 of the receptor when compared with the C-terminal α5 helix of G s . The conformation of the finger loop in βarr1 is different from that adopted by the finger loop of visual arrestin when it couples to rhodopsin 8 . β 1 AR coupled to βarr1 shows considerable differences in structure compared with β 1 AR coupled to Nb80, including an inward movement of extracellular loop 3 and the cytoplasmic ends of H5 and H6. We observe weakened interactions between formoterol and two serine residues in H5 at the orthosteric binding site of β 1 AR, and find that formoterol has a lower affinity for the β 1 AR-βarr1 complex than for the β 1 AR-G s complex. The structural differences between these complexes of β 1 AR provide a foundation for the design of small molecules that could bias signalling in the β-adrenoceptors.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin 1,Beta-1 adrenergic receptorA,
C [auth B]
416Escherichia coli K-12Meleagris gallopavo
This entity is chimeric
Mutation(s): 6 
Gene Names: trxAfipAtsnCb3781JW5856ADRB1
Membrane Entity: Yes 
UniProt
Find proteins for P07700 (Meleagris gallopavo)
Explore P07700 
Go to UniProtKB:  P07700
Find proteins for P0AA25 (Escherichia coli (strain K12))
Explore P0AA25 
Go to UniProtKB:  P0AA25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP07700P0AA25
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Camelid antibody fragment Nb80B [auth C],
D
121Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2CV
Query on 2CV

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
HEGA-10
C18 H37 N O7
ITEIKACYSCODFV-ATLSCFEFSA-N
H98
Query on H98

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B]
~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-ethyl]-2-oxidanyl-phenyl]methanamide
C19 H24 N2 O4
BPZSYCZIITTYBL-YJYMSZOUSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.277 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.65α = 90
b = 121.12β = 90
c = 129.84γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2CVClick on this verticalbar to view detailsBest fitted H98Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-08
    Changes: Database references
  • Version 1.3: 2020-08-12
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary