7WZ8

Structure of human langerin complex in Birbeck granules


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.40 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-electron tomography of Birbeck granules reveals the molecular mechanism of langerin lattice formation.

Oda, T.Yanagisawa, H.Shinmori, H.Ogawa, Y.Kawamura, T.

(2022) Elife 11: e79990-e79990

  • DOI: https://doi.org/10.7554/eLife.79990
  • Primary Citation of Related Structures:  
    7WZ8

  • PubMed Abstract: 

    Langerhans cells are specialized antigen-presenting cells localized within the epidermis and mucosal epithelium. Upon contact with Langerhans cells, pathogens are captured by the C-type lectin langerin and internalized into a structurally unique vesicle known as a Birbeck granule. Although the immunological role of Langerhans cells and Birbeck granules have been extensively studied, the mechanism by which the characteristic zippered membrane structure of Birbeck granules is formed remains elusive. In this study, we observed isolated Birbeck granules using cryo-electron tomography and reconstructed the 3D structure of the repeating unit of the honeycomb lattice of langerin at 6.4 Å resolution. We found that the interaction between the two langerin trimers was mediated by docking the flexible loop at residues 258-263 into the secondary carbohydrate-binding cleft. Mutations within the loop inhibited Birbeck granule formation and the internalization of HIV pseudovirus. These findings suggest a molecular mechanism for membrane zippering during Birbeck granule biogenesis and provide insight into the role of langerin in the defense against viral infection.


  • Organizational Affiliation

    Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, Chuo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SNAP-tag,C-type lectin domain family 4 member K551Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJ71 (Homo sapiens)
Explore Q9UJ71 
Go to UniProtKB:  Q9UJ71
PHAROS:  Q9UJ71
GTEx:  ENSG00000116031 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJ71
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.40 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2
RECONSTRUCTIONRELION4.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP21H02654

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references
  • Version 1.2: 2023-05-31
    Changes: Refinement description
  • Version 1.3: 2023-08-02
    Changes: Database references