3CAY

Crystal structure of Lipopeptide Detergent (LPD-12)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of a self-assembling lipopeptide detergent at 1.20 A.

Ho, D.N.Pomroy, N.C.Cuesta-Seijo, J.A.Prive, G.G.

(2008) Proc.Natl.Acad.Sci.USA 105: 12861-12866

  • DOI: 10.1073/pnas.0801941105

  • PubMed Abstract: 
  • Lipopeptide detergents (LPDs) are a new class of amphiphile designed specifically for the structural study of integral membrane proteins. The LPD monomer consists of a 25-residue peptide with fatty acyl chains linked to side chains located at positio ...

    Lipopeptide detergents (LPDs) are a new class of amphiphile designed specifically for the structural study of integral membrane proteins. The LPD monomer consists of a 25-residue peptide with fatty acyl chains linked to side chains located at positions 2 and 24 of the peptide. LPDs are designed to form alpha-helices that self-assemble into cylindrical micelles, providing a more natural interior acyl chain packing environment relative to traditional detergents. We have determined the crystal structure of LPD-12, an LPD coupled to two dodecanoic acids, to a resolution of 1.20 A. The LPD-12 monomers adopt the target conformation and associate into cylindrical octamers as expected. Pairs of helices are strongly associated as Alacoil-type antiparallel dimers, and four of these dimers interact through much looser contacts into assemblies with approximate D(2) symmetry. The aligned helices form a cylindrical shell with a hydrophilic exterior that protects an interior hydrophobic cavity containing the 16 LPD acyl chains. Over 90% of the methylene/methyl groups from the acylated side chains are visible in the micelle interiors, and approximately 90% of these adopt trans dihedral angle conformations. Dodecylmaltoside (DDM) was required for the crystallization of LPD-12, and we find 10-24 ordered DDM molecules associated with each LPD assembly, resulting in an overall micelle molecular weight of approximately 30 kDa. The structures confirm the major design objectives of the LPD framework, and reveal unexpected features that will be helpful in the engineering additional versions of lipopeptide amphiphiles.


    Organizational Affiliation

    Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, 101 College Street, Toronto, ON, Canada M5G 1L7.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LPD-12
A, B, C, D, E, F, G, H, I, J, K, L
27N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
O12
Query on O12
A, B, C, D, E, F, G, H, I, J, K, L
L-peptide linkingC17 H34 N2 O3

--

NH2
Query on NH2
A, B, C, D, E, F, G, H, I, J, K, L
NON-POLYMERH2 N

--

ACE
Query on ACE
A, B, C, D, E, F, G, H, I, J, K, L
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.134 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.484α = 90.00
b = 130.040β = 90.00
c = 42.807γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance