4AKM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

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This is version 1.4 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: https://doi.org/10.1186/1741-7007-10-62
  • Primary Citation of Related Structures:  
    4AKM

  • 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 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. The crystal structure of the conserved domain of human DC-LAMP was solved. It is the first high-resolution structure of a heavily glycosylated lysosomal membrane protein. The structure represents a novel β-prism fold formed by two β-sheets bent by β-bulges and connected by a disulfide bond. Flexible loops and a hydrophobic pocket represent possible sites of molecular interaction. Computational models of the glycosylated luminal regions of LAMP-1 and LAMP-2 indicate that the proteins adopt a compact conformation in close proximity to the lysosomal membrane. The models correspond to the thickness of the lysosomal glycoprotein coat of only 5 to 12 nm, according to electron microscopy. The conserved luminal domain of lysosome-associated membrane proteins forms a previously unknown β-prism fold. Insights into the structure of the lysosomal glycoprotein coat were obtained by computational models of the LAMP-1 and LAMP-2 luminal regions.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN 3
A, B
166Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQV4 (Homo sapiens)
Explore Q9UQV4 
Go to UniProtKB:  Q9UQV4
PHAROS:  Q9UQV4
GTEx:  ENSG00000078081 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQV4
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q9UQV4-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.6α = 90
b = 52.6β = 90
c = 141.98γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2017-07-12
    Changes: Refinement description
  • Version 1.2: 2019-07-17
    Changes: Data collection, Derived calculations
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2024-10-09
    Changes: Data collection, Database references, Structure summary