6H7J

ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND AGONIST ISOPRENALINE AND NANOBODY Nb80


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.285 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular basis for high-affinity agonist binding in GPCRs.

Warne, T.Edwards, P.C.Dore, A.S.Leslie, A.G.W.Tate, C.G.

(2019) Science 364: 775-778

  • DOI: 10.1126/science.aau5595
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • G protein-coupled receptors (GPCRs) in the G protein-coupled active state have higher affinity for agonists as compared with when they are in the inactive state, but the molecular basis for this is unclear. We have determined four active-state struct ...

    G protein-coupled receptors (GPCRs) in the G protein-coupled active state have higher affinity for agonists as compared with when they are in the inactive state, but the molecular basis for this is unclear. We have determined four active-state structures of the β 1 -adrenoceptor (β 1 AR) bound to conformation-specific nanobodies in the presence of agonists of varying efficacy. Comparison with inactive-state structures of β 1 AR bound to the identical ligands showed a 24 to 42% reduction in the volume of the orthosteric binding site. Potential hydrogen bonds were also shorter, and there was up to a 30% increase in the number of atomic contacts between the receptor and ligand. This explains the increase in agonist affinity of GPCRs in the active state for a wide range of structurally distinct agonists.


    Organizational Affiliation

    Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6GT, UK.,Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.,Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. cgt@mrc-lmb.cam.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thioredoxin 1
E, F
109Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: trxA (fipA, tsnC)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
β1 adrenergic receptor (engineered)
Find proteins for P0AA25 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA25
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-1 adrenergic receptor
A, B
307Meleagris gallopavoMutation(s): 6 
Gene Names: ADRB1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
β1 adrenergic receptor (engineered)
Find proteins for P07700 (Meleagris gallopavo)
Go to Gene View: ADRB1
Go to UniProtKB:  P07700
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Camelid antibody fragment Nb80
C, D
121N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
5FW
Query on 5FW

Download SDF File 
Download CCD File 
A, B
ISOPRENALINE
C11 H17 N O3
JWZZKOKVBUJMES-NSHDSACASA-N
 Ligand Interaction
2CV
Query on 2CV

Download SDF File 
Download CCD File 
A, B
HEGA-10
C18 H37 N O7
ITEIKACYSCODFV-ATLSCFEFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.285 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 116.727α = 90.00
b = 121.183β = 90.00
c = 129.539γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Derived calculations
  • Version 1.2: 2019-05-22
    Type: Data collection, Database references
  • Version 1.3: 2019-06-05
    Type: Data collection, Database references