6H7O

ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND WEAK PARTIAL AGONIST CYANOPINDOLOL AND NANOBODY Nb6B9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

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:  
    6H7M, 6H7O, 6H7J, 6H7L

  • 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thioredoxin 1EF109Escherichia coli K-12Mutation(s): 2 
Gene Names: trxAfipAtsnCb3781JW5856
Find proteins for P0AA25 (Escherichia coli (strain K12))
Explore P0AA25 
Go to UniProtKB:  P0AA25
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-1 adrenergic receptorAB307Meleagris gallopavoMutation(s): 6 
Gene Names: ADRB1
Find proteins for P07700 (Meleagris gallopavo)
Explore P07700 
Go to UniProtKB:  P07700
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Camelid antibody fragment Nb6B9CD121Lama glamaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2CV
Query on 2CV

Download CCD File 
A, B
HEGA-10
C18 H37 N O7
ITEIKACYSCODFV-ATLSCFEFSA-N
 Ligand Interaction
P32
Query on P32

Download CCD File 
A, B
4-{[(2S)-3-(tert-butylamino)-2-hydroxypropyl]oxy}-3H-indole-2-carbonitrile
C16 H21 N3 O2
CQEFAUFOQSCRMZ-LBPRGKRZSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.573α = 90
b = 119.963β = 90
c = 130.096γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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