3U90

apoferritin: complex with SDS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Beyond the detergent effect: a binding site for sodium dodecyl sulfate (SDS) in mammalian apoferritin.

Liu, R.Bu, W.Xi, J.Mortazavi, S.R.Cheung-Lau, J.C.Dmochowski, I.J.Loll, P.J.

(2012) Acta Crystallogr.,Sect.D 68: 497-504

  • DOI: 10.1107/S0907444912002740

  • PubMed Abstract: 
  • Although sodium dodecyl sulfate (SDS) is widely used as an anionic detergent, it can also exert specific pharmacological effects that are independent of the surfactant properties of the molecule. However, structural details of how proteins recognize ...

    Although sodium dodecyl sulfate (SDS) is widely used as an anionic detergent, it can also exert specific pharmacological effects that are independent of the surfactant properties of the molecule. However, structural details of how proteins recognize SDS are scarce. Here, it is demonstrated that SDS binds specifically to a naturally occurring four-helix bundle protein: horse apoferritin. The X-ray crystal structure of the apoferritin-SDS complex was determined at a resolution of 1.9 Å and revealed that the SDS binds in an internal cavity that has previously been shown to recognize various general anesthetics. A dissociation constant of 24 ± 9 µM at 293 K was determined by isothermal titration calorimetry. SDS binds in this cavity by bending its alkyl tail into a horseshoe shape; the charged SDS head group lies in the opening of the cavity at the protein surface. This crystal structure provides insights into the protein-SDS interactions that give rise to binding and may prove useful in the design of novel SDS-like ligands for some proteins.


    Organizational Affiliation

    Department of Anesthesia and Critical Care, University of Pennsylvania, Philadelphia, Pennsylvania, USA. renyu.liu@uphs.upenn.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferritin light chain
A
174Equus caballusMutation(s): 0 
Gene Names: FTL
Find proteins for P02791 (Equus caballus)
Go to Gene View: FTL
Go to UniProtKB:  P02791
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SDS
Query on SDS

Download SDF File 
Download CCD File 
A
DODECYL SULFATE
C12 H26 O4 S
MOTZDAYCYVMXPC-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SDSKd: 24000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.185 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 181.830α = 90.00
b = 181.830β = 90.00
c = 181.830γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
CNSphasing
ADSCdata collection
d*TREKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Database references
  • Version 1.2: 2019-07-17
    Type: Data collection, Derived calculations, Refinement description