5D6L

beta2AR-T4L - CIM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The cubicon method for concentrating membrane proteins in the cubic mesophase.

Ma, P.Weichert, D.Aleksandrov, L.A.Jensen, T.J.Riordan, J.R.Liu, X.Kobilka, B.K.Caffrey, M.

(2017) Nat Protoc 12: 1745-1762

  • DOI: 10.1038/nprot.2017.057
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The lipid cubic phase (in meso) method is an important approach for generating crystals and high-resolution X-ray structures of integral membrane proteins. However, as a consequence of instability, it can be impossible-using traditional methods-to co ...

    The lipid cubic phase (in meso) method is an important approach for generating crystals and high-resolution X-ray structures of integral membrane proteins. However, as a consequence of instability, it can be impossible-using traditional methods-to concentrate certain membrane proteins and complexes to values suitable for in meso crystallization and structure determination. The cubicon method described here exploits the amphiphilic nature of membrane proteins and their natural tendency to partition preferentially into lipid bilayers from aqueous solution. Using several rounds of reconstitution, the protein concentration in the bilayer of the cubic mesophase can be ramped up stepwise from less than a milligram per milliliter to tens of milligrams per milliliter for crystallogenesis. The general applicability of the method is demonstrated with five integral membrane proteins: the β2-adrenergic G protein-coupled receptor (β2AR), the peptide transporter (PepTSt), diacylglycerol kinase (DgkA), the alginate transporter (AlgE) and the cystic fibrosis transmembrane conductance regulator (CFTR). In the cases of β2AR, PepTSt, DgkA and AlgE, an effective 20- to 45-fold concentration was realized, resulting in a protein-laden mesophase that allowed the formation of crystals using the in meso method and structure determination to resolutions ranging from 2.4 Å to 3.2 Å. In addition to opening up in meso crystallization to a broader range of integral membrane protein targets, the cubicon method should find application in situations that require membrane protein reconstitution in a lipid bilayer at high concentrations. These applications include functional and biophysical characterization studies for ligand screening, drug delivery, antibody production and protein complex formation. A typical cubicon experiment can be completed in 3-5 h.


    Organizational Affiliation

    Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-2 adrenergic receptor,Endolysin,Beta-2 adrenergic receptor
A
500Enterobacteria phage T4Homo sapiens
This entity is chimeric
Mutation(s): 1 
Gene Names: E, ADRB2 (ADRB2R, B2AR)
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Find proteins for P07550 (Homo sapiens)
Go to Gene View: ADRB2
Go to UniProtKB:  P07550
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BU1
Query on BU1

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A
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
ACM
Query on ACM

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A
ACETAMIDE
C2 H5 N O
DLFVBJFMPXGRIB-UHFFFAOYSA-N
 Ligand Interaction
N9S
Query on N9S

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A
4-O-alpha-D-Glucopyranosyl-beta-D-glucopyranose
Beta-Maltose
C12 H22 O11
GUBGYTABKSRVRQ-QUYVBRFLSA-N
 Ligand Interaction
12P
Query on 12P

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A
DODECAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C24 H50 O13
WRZXKWFJEFFURH-UHFFFAOYSA-N
 Ligand Interaction
CAU
Query on CAU

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A
(2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
(S)-Carazolol
C18 H22 N2 O2
BQXQGZPYHWWCEB-ZDUSSCGKSA-N
 Ligand Interaction
PLM
Query on PLM

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A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
CLR
Query on CLR

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A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 107.260α = 90.00
b = 170.360β = 105.67
c = 40.270γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-08-12 
  • Released Date: 2016-08-17 
  • Deposition Author(s): Ma, P., Caffrey, M.

Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland12/IA/1255
Belgian National Funds for Scientific ResearchBelgiumWELBIO CR-2012S-04

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Database references