3F33

Apoferritin: complex with propofol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A unitary anesthetic binding site at high resolution.

Vedula, L.S.Brannigan, G.Economou, N.J.Xi, J.Hall, M.A.Liu, R.Rossi, M.J.Dailey, W.P.Grasty, K.C.Klein, M.L.Eckenhoff, R.G.Loll, P.J.

(2009) J Biol Chem 284: 24176-24184

  • DOI: 10.1074/jbc.M109.017814
  • Primary Citation of Related Structures:  
    3F32, 3F33, 3F34, 3F35, 3F36, 3F37, 3F38, 3F39

  • PubMed Abstract: 
  • Propofol is the most widely used injectable general anesthetic. Its targets include ligand-gated ion channels such as the GABA(A) receptor, but such receptor-channel complexes remain challenging to study at atomic resolution. Until structural biology methods advance to the point of being able to deal with systems such as the GABA(A) receptor, it will be necessary to use more tractable surrogates to probe the molecular details of anesthetic recognition ...

    Propofol is the most widely used injectable general anesthetic. Its targets include ligand-gated ion channels such as the GABA(A) receptor, but such receptor-channel complexes remain challenging to study at atomic resolution. Until structural biology methods advance to the point of being able to deal with systems such as the GABA(A) receptor, it will be necessary to use more tractable surrogates to probe the molecular details of anesthetic recognition. We have previously shown that recognition of inhalational general anesthetics by the model protein apoferritin closely mirrors recognition by more complex and clinically relevant protein targets; here we show that apoferritin also binds propofol and related GABAergic anesthetics, and that the same binding site mediates recognition of both inhalational and injectable anesthetics. Apoferritin binding affinities for a series of propofol analogs were found to be strongly correlated with the ability to potentiate GABA responses at GABA(A) receptors, validating this model system for injectable anesthetics. High resolution x-ray crystal structures reveal that, despite the presence of hydrogen bond donors and acceptors, anesthetic recognition is mediated largely by van der Waals forces and the hydrophobic effect. Molecular dynamics simulations indicate that the ligands undergo considerable fluctuations about their equilibrium positions. Finally, apoferritin displays both structural and dynamic responses to anesthetic binding, which may mimic changes elicited by anesthetics in physiologic targets like ion channels.


    Organizational Affiliation

    Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferritin light chainA174Equus caballusMutation(s): 0 
Gene Names: FTL
UniProt
Find proteins for P02791 (Equus caballus)
Explore P02791 
Go to UniProtKB:  P02791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02791
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PFL
Query on PFL

Download Ideal Coordinates CCD File 
H [auth A]2,6-BIS(1-METHYLETHYL)PHENOL
C12 H18 O
OLBCVFGFOZPWHH-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PFL PDBBind:  3F33 Kd: 4.60e+5 (nM) from 1 assay(s)
Binding MOAD:  3F33 Kd: 4.60e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.487α = 90
b = 182.487β = 90
c = 182.487γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance