6TKO

Phosphorylated turkey beta1 adrenoceptor with bound agonist formoterol coupled to arrestin-2 in lipid nanodisc.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 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
Beta-1 adrenergic receptor328Meleagris gallopavoMutation(s): 9 
Gene Names: ADRB1
Membrane Entity: Yes 
UniProt
Find proteins for P07700 (Meleagris gallopavo)
Explore P07700 
Go to UniProtKB:  P07700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07700
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-arrestin-1418Homo sapiensMutation(s): 3 
Gene Names: ARRB1ARR1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P49407 (Homo sapiens)
Explore P49407 
Go to UniProtKB:  P49407
PHAROS:  P49407
GTEx:  ENSG00000137486 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49407
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab30 heavy chainC [auth H]237Phage display vector pTDispMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab30 light chainD [auth L]215Phage display vector pTDispMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H98 (Subject of Investigation/LOI)
Query on H98

Download Ideal Coordinates CCD File 
E [auth A]~{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
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.17.1-3660
MODEL REFINEMENTREFMAC5

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)United KingdomEMPSI 339995
Medical Research Council (MRC, United Kingdom)United KingdomMRC U105197215

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2020-08-12
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Refinement description, Structure summary