2YG2

Structure of apolioprotein M in complex with Sphingosine 1-Phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Endothelium-Protective Sphingosine-1-Phosphate Provided by Hdl-Associated Apolipoprotein M.

Christoffersen, C.Obinata, H.Kumaraswamy, S.B.Galvani, S.Ahnstrom, J.Sevvana, M.Egerer-Sieber, C.Muller, Y.A.Hla, T.Nielsen, L.B.Dahlback, B.

(2011) Proc.Natl.Acad.Sci.USA 108: 9613

  • DOI: 10.1073/pnas.1103187108

  • PubMed Abstract: 
  • Protection of the endothelium is provided by circulating sphingosine-1-phosphate (S1P), which maintains vascular integrity. We show that HDL-associated S1P is bound specifically to both human and murine apolipoprotein M (apoM). Thus, isolated human A ...

    Protection of the endothelium is provided by circulating sphingosine-1-phosphate (S1P), which maintains vascular integrity. We show that HDL-associated S1P is bound specifically to both human and murine apolipoprotein M (apoM). Thus, isolated human ApoM(+) HDL contained S1P, whereas ApoM(-) HDL did not. Moreover, HDL in Apom(-/-) mice contains no S1P, whereas HDL in transgenic mice overexpressing human apoM has an increased S1P content. The 1.7-Å structure of the S1P-human apoM complex reveals that S1P interacts specifically with an amphiphilic pocket in the lipocalin fold of apoM. Human ApoM(+) HDL induced S1P(1) receptor internalization, downstream MAPK and Akt activation, endothelial cell migration, and formation of endothelial adherens junctions, whereas apoM(-) HDL did not. Importantly, lack of S1P in the HDL fraction of Apom(-/-) mice decreased basal endothelial barrier function in lung tissue. Our results demonstrate that apoM, by delivering S1P to the S1P(1) receptor on endothelial cells, is a vasculoprotective constituent of HDL.


    Organizational Affiliation

    Department of Clinical Biochemistry, Rigshospitalet, 2100 Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
APOLIPOPROTEIN M
A, B
172Homo sapiensMutation(s): 0 
Gene Names: APOM (G3A, NG20)
Find proteins for O95445 (Homo sapiens)
Go to Gene View: APOM
Go to UniProtKB:  O95445
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
S1P
Query on S1P

Download SDF File 
Download CCD File 
A, B
(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
sphingosine 1-phosphate
C18 H38 N O5 P
DUYSYHSSBDVJSM-KRWOKUGFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FLCIC50: 900 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.191 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 68.280α = 90.00
b = 68.280β = 90.00
c = 135.580γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-06-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance