4AKM

Crystal structure of the human lysosome-associated membrane protein LAMP-3 (aka DC-LAMP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.687 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of the Conserved Domain of the Dc Lysosomal Associated Membrane Protein: Implications for the Lysosomal Glycocalyx.

Wilke, S.Krausze, J.Bussow, K.

(2012) Bmc Biol. 10: 62

  • DOI: 10.1186/1741-7007-10-62

  • PubMed Abstract: 
  • The family of lysosome-associated membrane proteins (LAMP) comprises the multifunctional, ubiquitous LAMP-1 and LAMP-2, and the cell type-specific proteins DC-LAMP (LAMP-3), BAD-LAMP (UNC-46, C20orf103) and macrosialin (CD68). LAMPs have been implica ...

    The family of lysosome-associated membrane proteins (LAMP) comprises the multifunctional, ubiquitous LAMP-1 and LAMP-2, and the cell type-specific proteins DC-LAMP (LAMP-3), BAD-LAMP (UNC-46, C20orf103) and macrosialin (CD68). LAMPs have been implicated in a multitude of cellular processes, including phagocytosis, autophagy, lipid transport and aging. LAMP-2 isoform A acts as a receptor in chaperone-mediated autophagy. LAMP-2 deficiency causes the fatal Danon disease. The abundant proteins LAMP-1 and LAMP-2 are major constituents of the glycoconjugate coat present on the inside of the lysosomal membrane, the 'lysosomal glycocalyx'. The LAMP family is characterized by a conserved domain of 150 to 200 amino acids with two disulfide bonds.


    Organizational Affiliation

    Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Inhoffenstr, 7, 38124 Braunschweig, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN 3
A, B
166Homo sapiensMutation(s): 0 
Gene Names: LAMP3 (DCLAMP, TSC403)
Find proteins for Q9UQV4 (Homo sapiens)
Go to Gene View: LAMP3
Go to UniProtKB:  Q9UQV4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IR3
Query on IR3

Download SDF File 
Download CCD File 
A, B
IRIDIUM (III) ION
Ir
MILUBEOXRNEUHS-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.687 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.227 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 52.600α = 90.00
b = 52.600β = 90.00
c = 141.980γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2017-07-12
    Type: Refinement description