3K2S

Solution structure of double super helix model


Experimental Data Snapshot

  • Method: SOLUTION SCATTERING

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1074/jbc.M109.039537
  • Primary Citation of Related Structures:  
    3K2S

  • 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) 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; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, Ohio 44195; Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio 44195. Electronic address: hazens@ccf.org.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apolipoprotein A-I
A, B
243Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02647 (Homo sapiens)
Explore P02647 
Go to UniProtKB:  P02647
PHAROS:  P02647
GTEx:  ENSG00000118137 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02647
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth B]
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth B],
AF [auth B],
AG [auth B],
AH [auth B],
BA [auth A],
BB [auth A],
BC [auth A],
BE [auth B],
BF [auth B],
BG [auth B],
BH [auth B],
C [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
CE [auth B],
CF [auth B],
CG [auth B],
CH [auth B],
D [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
DE [auth B],
DF [auth B],
DG [auth B],
DH [auth B],
E [auth A],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth B],
EF [auth B],
EG [auth B],
F [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth B],
FF [auth B],
FG [auth B],
G [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth B],
GF [auth B],
GG [auth B],
H [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth B],
HF [auth B],
HG [auth B],
I [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth B],
IF [auth B],
IG [auth B],
J [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth B],
JF [auth B],
JG [auth B],
K [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth B],
KF [auth B],
KG [auth B],
L [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth B],
LF [auth B],
LG [auth B],
M [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth B],
MF [auth B],
MG [auth B],
N [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth B],
NF [auth B],
NG [auth B],
O [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth B],
OF [auth B],
OG [auth B],
P [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PE [auth B],
PF [auth B],
PG [auth B],
Q [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QE [auth B],
QF [auth B],
QG [auth B],
R [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RE [auth B],
RF [auth B],
RG [auth B],
S [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SE [auth B],
SF [auth B],
SG [auth B],
T [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth B],
TE [auth B],
TF [auth B],
TG [auth B],
U [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth B],
UE [auth B],
UF [auth B],
UG [auth B],
V [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth B],
VE [auth B],
VF [auth B],
VG [auth B],
W [auth A],
WA [auth A],
WB [auth A],
WD [auth B],
WE [auth B],
WF [auth B],
WG [auth B],
X [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth B],
XE [auth B],
XF [auth B],
XG [auth B],
Y [auth A],
YA [auth A],
YB [auth A],
YD [auth B],
YE [auth B],
YF [auth B],
YG [auth B],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZD [auth B],
ZE [auth B],
ZF [auth B],
ZG [auth B]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
BD [auth A]
CD [auth A]
DD [auth A]
EH [auth B]
FH [auth B]
BD [auth A],
CD [auth A],
DD [auth A],
EH [auth B],
FH [auth B],
GH [auth B],
HH [auth B],
IH [auth B],
JH [auth B],
KH [auth B],
LH [auth B],
MH [auth B],
NH [auth B],
PD [auth A],
QD [auth A],
RD [auth A],
SD [auth A],
WC [auth A],
YC [auth A],
ZC [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION SCATTERING

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations