1LSH

LIPID-PROTEIN INTERACTIONS IN LIPOVITELLIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Lipid-protein interactions in lipovitellin.

Thompson, J.R.Banaszak, L.J.

(2002) Biochemistry 41: 9398-9409


  • PubMed Abstract: 
  • The refined molecular structure of lipovitellin is described using synchrotron cryocrystallographic data to 1.9 A resolution. Lipovitellin is the predominant lipoprotein found in the yolk of egg-laying animals and is involved in lipid and metal stora ...

    The refined molecular structure of lipovitellin is described using synchrotron cryocrystallographic data to 1.9 A resolution. Lipovitellin is the predominant lipoprotein found in the yolk of egg-laying animals and is involved in lipid and metal storage. It is thought to be related in amino acid sequence to segments of apolipoprotein B and the microsomal transfer protein responsible for the assembly of low-density lipoproteins. Lipovitellin contains a heterogeneous mixture of about 16% (w/w) noncovalently bound lipid, mostly phospholipid. Previous X-ray structural studies at ambient temperature described several different protein domains including a large cavity in each subunit of the dimeric protein. The cavity was free of any visible electron density for lipid molecules at room temperature, suggesting that only dynamic interactions exist with the protein. An important result from this crystallographic study at 100 K is the appearance of some bound ordered lipid along the walls of the binding cavity. The precise identification of the lipid type is difficult because of discontinuities in the electron density. Nonetheless, the conformations of 7 phospholipids and 43 segments of hydrocarbon chains greater than 5 atoms in length have been discovered. The conformations of the bound lipid and the interactions between protein and lipid provide insights into the factors governing lipoprotein formation.


    Related Citations: 
    • The Structural Basis of Lipid Interactions in Lipovitellin, a Souble Lipoprotein
      Anderson, T.A.,Levitt, D.G.,Banaszak, L.J.
      (1998) Structure 6: 895


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LIPOVITELLIN (LV-1N, LV-1C)
A
1056Ichthyomyzon unicuspisN/A
Find proteins for Q91062 (Ichthyomyzon unicuspis)
Go to UniProtKB:  Q91062
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LIPOVITELLIN (LV-2)
B
319Ichthyomyzon unicuspisN/A
Find proteins for Q91062 (Ichthyomyzon unicuspis)
Go to UniProtKB:  Q91062
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLD
Query on PLD

Download SDF File 
Download CCD File 
A, B
DIUNDECYL PHOSPHATIDYL CHOLINE
C50 H101 N O8 P
QFFSGJSMHPWZOB-QSCHNALKSA-O
 Ligand Interaction
UPL
Query on UPL

Download SDF File 
Download CCD File 
A, B
UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID
UNKNOWN PHOSPHOLIPID FRAGMENT
C34 H70
QPCSNFPFMCVVAI-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 190.170α = 90.00
b = 84.520β = 100.39
c = 89.530γ = 90.00
Software Package:
Software NamePurpose
1.0refinement
HKL-2000data reduction
HKL-2000data collection
CNSphasing
CNSrefinement
1.1refinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-07-31
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance