5JTB

Crystal structure of the chimeric protein of A2aAR-BRIL with bound iodide ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Fast iodide-SAD phasing for high-throughput membrane protein structure determination.

Melnikov, I.Polovinkin, V.Kovalev, K.Gushchin, I.Shevtsov, M.Shevchenko, V.Mishin, A.Alekseev, A.Rodriguez-Valera, F.Borshchevskiy, V.Cherezov, V.Leonard, G.A.Gordeliy, V.Popov, A.

(2017) Sci Adv 3: e1602952-e1602952

  • DOI: 10.1126/sciadv.1602952
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide-single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a comm ...

    We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide-single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins-the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein-coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques.


    Organizational Affiliation

    Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, F-38000 Grenoble, France.,Departments of Chemistry, Biological Sciences, and Physics & Astronomy, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.,Department of Vegetal Production and Microbiology, Universidad Miguel Hernández de Elche, San Juan de Alicante, Valencia, Spain.,European Synchrotron Radiation Facility, 38043 Grenoble, France.,Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russia.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
A
447Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: cybC, ADORA2A (ADORA2)
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P29274 (Homo sapiens)
Go to Gene View: ADORA2A
Go to UniProtKB:  P29274
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLB
Query on OLB

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A
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
 Ligand Interaction
OLC
Query on OLC

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A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
IOD
Query on IOD

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A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
OLA
Query on OLA

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A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
ZMA
Query on ZMA

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A
4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol
C16 H15 N7 O2
PWTBZOIUWZOPFT-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-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: 2.8 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.234 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 39.648α = 90.00
b = 179.793β = 90.00
c = 139.810γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
SHELXCDphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release