4BVN | pdb_00004bvn

Ultra-thermostable beta1-adrenoceptor with cyanopindolol bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.246 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

The 2.1 A Resolution Structure of Cyanopindolol-Bound Beta1- Adrenoceptor Identifies an Intramembrane Na+ Ion that Stabilises the Ligand-Free Receptor.

Miller-Gallacher, J.L.Nehme, R.Warne, T.Edwards, P.C.Schertler, G.F.X.Leslie, A.G.W.Tate, C.G.

(2014) PLoS One 9: 92727

  • DOI: https://doi.org/10.1371/journal.pone.0092727
  • Primary Citation Related Structures: 
    4BVN

  • PubMed Abstract: 

    The β1-adrenoceptor (β1AR) is a G protein-coupled receptor (GPCR) that is activated by the endogenous agonists adrenaline and noradrenaline. We have determined the structure of an ultra-thermostable β1AR mutant bound to the weak partial agonist cyanopindolol to 2.1 Å resolution. High-quality crystals (100 μm plates) were grown in lipidic cubic phase without the assistance of a T4 lysozyme or BRIL fusion in cytoplasmic loop 3, which is commonly employed for GPCR crystallisation. An intramembrane Na+ ion was identified co-ordinated to Asp872.50, Ser1283.39 and 3 water molecules, which is part of a more extensive network of water molecules in a cavity formed between transmembrane helices 1, 2, 3, 6 and 7. Remarkably, this water network and Na+ ion is highly conserved between β1AR and the adenosine A2A receptor (rmsd of 0.3 Å), despite an overall rmsd of 2.4 Å for all Cα atoms and only 23% amino acid identity in the transmembrane regions. The affinity of agonist binding and nanobody Nb80 binding to β1AR is unaffected by Na+ ions, but the stability of the receptor is decreased by 7.5°C in the absence of Na+. Mutation of amino acid side chains that are involved in the co-ordination of either Na+ or water molecules in the network decreases the stability of β1AR by 5-10°C. The data suggest that the intramembrane Na+ and associated water network stabilise the ligand-free state of β1AR, but still permits the receptor to form the activated state which involves the collapse of the Na+ binding pocket on agonist binding.


  • Organizational Affiliation
    • Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, Cambridgeshire, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 38.91 kDa 
  • Atom Count: 2,506 
  • Modeled Residue Count: 289 
  • Deposited Residue Count: 315 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-1 ADRENERGIC RECEPTOR315Meleagris gallopavoMutation(s): 11 
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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC

Query on OLC



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
P32

Query on P32



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

Query on MHA



Download:Ideal Coordinates CCD File
E [auth A](CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID
C6 H10 N2 O5
QZTKDVCDBIDYMD-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.246 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.093α = 90
b = 62.127β = 90
c = 95.776γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.2: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary
  • Version 1.5: 2025-07-16
    Changes: Derived calculations, Structure summary