3K2S

Solution structure of double super helix model


Experimental Data Snapshot

  • Method: SOLUTION SCATTERING

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Double superhelix model of high density lipoprotein.

Wu, Z.Gogonea, V.Lee, X.Wagner, M.A.Li, X.M.Huang, Y.Undurti, A.May, R.P.Haertlein, M.Moulin, M.Gutsche, I.Zaccai, G.Didonato, J.A.Hazen, S.L.

(2009) J.Biol.Chem. 284: 36605-36619

  • DOI: 10.1074/jbc.M109.039537

  • PubMed Abstract: 
  • High density lipoprotein (HDL), the carrier of so-called "good" cholesterol, serves as the major athero-protective lipoprotein and has emerged as a key therapeutic target for cardiovascular disease. We applied small angle neutron scattering (SANS) wi ...

    High density lipoprotein (HDL), the carrier of so-called "good" cholesterol, serves as the major athero-protective lipoprotein and has emerged as a key therapeutic target for cardiovascular disease. We applied small angle neutron scattering (SANS) with contrast variation and selective isotopic deuteration to the study of nascent HDL to obtain the low resolution structure in solution of the overall time-averaged conformation of apolipoprotein AI (apoA-I) versus the lipid (acyl chain) core of the particle. Remarkably, apoA-I is observed to possess an open helical shape that wraps around a central ellipsoidal lipid phase. Using the low resolution SANS shapes of the protein and lipid core as scaffolding, an all-atom computational model for the protein and lipid components of nascent HDL was developed by integrating complementary structural data from hydrogen/deuterium exchange mass spectrometry and previously published constraints from multiple biophysical techniques. Both SANS data and the new computational model, the double superhelix model, suggest an unexpected structural arrangement of protein and lipids of nascent HDL, an anti-parallel double superhelix wrapped around an ellipsoidal lipid phase. The protein and lipid organization in nascent HDL envisages a potential generalized mechanism for lipoprotein biogenesis and remodeling, biological processes critical to sterol and lipid transport, organismal energy metabolism, and innate immunity.


    Organizational Affiliation

    Department of Cell Biology, Cleveland Clinic, Cleveland, Ohio 44195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apolipoprotein A-I
A, B
243Homo sapiensMutation(s): 0 
Gene Names: APOA1
Find proteins for P02647 (Homo sapiens)
Go to Gene View: APOA1
Go to UniProtKB:  P02647
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

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Download CCD File 
A, B
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
POPC
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
 Ligand Interaction
CLR
Query on CLR

Download SDF File 
Download CCD File 
A, B
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION SCATTERING
Software Package:
Software NamePurpose
GROMACSrefinement
ILLdata reduction
ILLdata scaling
PRIMUSphasing
GNOMphasing
ILLdata collection
DEXANALrefinement
GNOMmodel building
DAMMINphasing
DAMMINmodel building
SASSIMrefinement
PRIMUSmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-21
    Type: Database references