4F7B | pdb_00004f7b

Structure of the lysosomal domain of limp-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.232 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Structure of LIMP-2 provides functional insights with implications for SR-BI and CD36.

Neculai, D.Schwake, M.Ravichandran, M.Zunke, F.Collins, R.F.Peters, J.Neculai, M.Plumb, J.Loppnau, P.Pizarro, J.C.Seitova, A.Trimble, W.S.Saftig, P.Grinstein, S.Dhe-Paganon, S.

(2013) Nature 504: 172-176

  • DOI: https://doi.org/10.1038/nature12684
  • Primary Citation Related Structures: 
    4F7B

  • PubMed Abstract: 

    Members of the CD36 superfamily of scavenger receptor proteins are important regulators of lipid metabolism and innate immunity. They recognize normal and modified lipoproteins, as well as pathogen-associated molecular patterns. The family consists of three members: SR-BI (which delivers cholesterol to the liver and steroidogenic organs and is a co-receptor for hepatitis C virus), LIMP-2/LGP85 (which mediates lysosomal delivery of β-glucocerebrosidase and serves as a receptor for enterovirus 71 and coxsackieviruses) and CD36 (a fatty-acid transporter and receptor for phagocytosis of effete cells and Plasmodium-infected erythrocytes). Notably, CD36 is also a receptor for modified lipoproteins and β-amyloid, and has been implicated in the pathogenesis of atherosclerosis and of Alzheimer's disease. Despite their prominent roles in health and disease, understanding the function and abnormalities of the CD36 family members has been hampered by the paucity of information about their structure. Here we determine the crystal structure of LIMP-2 and infer, by homology modelling, the structure of SR-BI and CD36. LIMP-2 shows a helical bundle where β-glucocerebrosidase binds, and where ligands are most likely to bind to SR-BI and CD36. Remarkably, the crystal structure also shows the existence of a large cavity that traverses the entire length of the molecule. Mutagenesis of SR-BI indicates that the cavity serves as a tunnel through which cholesterol(esters) are delivered from the bound lipoprotein to the outer leaflet of the plasma membrane. We provide evidence supporting a model whereby lipidic constituents of the ligands attached to the receptor surface are handed off to the membrane through the tunnel, accounting for the selective lipid transfer characteristic of SR-BI and CD36.


  • Organizational Affiliation
    • Cell Biology Program, The Hospital for Sick Children, Toronto M5G 1X8, Canada.

Macromolecule Content 

  • Total Structure Weight: 312.71 kDa 
  • Atom Count: 19,810 
  • Modeled Residue Count: 2,333 
  • Deposited Residue Count: 2,538 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysosome membrane protein 2
A, B, C, D, E
A, B, C, D, E, F
423Homo sapiensMutation(s): 0 
Gene Names: CD36L2LIMPIISCARB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14108 (Homo sapiens)
Explore Q14108 
Go to UniProtKB:  Q14108
PHAROS:  Q14108
GTEx:  ENSG00000138760 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14108
Glycosylation
Glycosylation Sites: 8Go to GlyGen: Q14108-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseBA [auth b],
CA [auth c],
G,
X
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, T
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G10133VD
GlyCosmos: G10133VD
GlyGen: G10133VD
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
EA [auth e],
FA [auth f],
I,
K,
AA [auth a],
EA [auth e],
FA [auth f],
I,
K,
N,
P,
U
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
GA [auth g],
J,
L,
O,
Q,
GA [auth g],
J,
L,
O,
Q,
R,
S,
V,
W,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M, Y
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G61751GZ
GlyCosmos: G61751GZ
GlyGen: G61751GZ
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseDA [auth d]5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AB [auth F]
BB [auth F]
HA [auth A]
IA [auth A]
JA [auth A]
AB [auth F],
BB [auth F],
HA [auth A],
IA [auth A],
JA [auth A],
MA [auth B],
NA [auth B],
OA [auth B],
PA [auth B],
RA [auth C],
SA [auth C],
UA [auth D],
WA [auth E],
YA [auth F],
ZA [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
DB [auth F],
LA [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
CB [auth F]
KA [auth A]
QA [auth B]
TA [auth C]
VA [auth D]
CB [auth F],
KA [auth A],
QA [auth B],
TA [auth C],
VA [auth D],
XA [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.232 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.772α = 90
b = 115.984β = 96.38
c = 145.084γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHARPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Structure summary
  • Version 1.2: 2013-11-20
    Changes: Database references
  • Version 1.3: 2013-12-18
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-11-27
    Changes: Data collection, Database references, Structure summary