4AKM

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

• PDB DOI: https://doi.org/10.2210/pdb4AKM/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2012-02-24 Released: 2012-08-15 
• Deposition Author(s): Krausze, J., Wilke, S., Buessow, K.

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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 

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

• PubMed: 22809326 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.52 kDa 
• Atom Count: 2,480 
• Modelled Residue Count: 312 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN 3	A, B	166	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQV4 (Homo sapiens) Explore Q9UQV4  Go to UniProtKB:  Q9UQV4
PHAROS:  Q9UQV4 GTEx:  ENSG00000078081

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
IR3	C [auth A], E [auth A], F [auth B], H [auth B]	IRIDIUM (III) ION Ir MILUBEOXRNEUHS-UHFFFAOYSA-N

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 = 52.6	α = 90
b = 52.6	β = 90
c = 141.98	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Krausze, J., Wilke, S., Buessow, K.

Revision History  

• 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