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- PDB-7wz8: Structure of human langerin complex in Birbeck granules -

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Basic information

Entry
Database: PDB / ID: 7wz8
TitleStructure of human langerin complex in Birbeck granules
ComponentsSNAP-tag,C-type lectin domain family 4 member K
KeywordsMEMBRANE PROTEIN / Birbeck granule / C-type lectin / Langerhans cell / virus defense
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / endocytic vesicle / clathrin-coated endocytic vesicle membrane / signaling receptor activity / early endosome membrane / carbohydrate binding / defense response to virus / external side of plasma membrane / plasma membrane
Similarity search - Function
CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
C-type lectin domain family 4 member K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 6.4 Å
AuthorsOda, T. / Yanagisawa, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21H02654 Japan
CitationJournal: Elife / Year: 2022
Title: Cryo-electron tomography of Birbeck granules reveals the molecular mechanism of langerin lattice formation.
Authors: Toshiyuki Oda / Haruaki Yanagisawa / Hideyuki Shinmori / Youichi Ogawa / Tatsuyoshi Kawamura /
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 ...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.
History
DepositionFeb 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 31, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Aug 2, 2023Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: SNAP-tag,C-type lectin domain family 4 member K
A: SNAP-tag,C-type lectin domain family 4 member K
B: SNAP-tag,C-type lectin domain family 4 member K
F: SNAP-tag,C-type lectin domain family 4 member K
D: SNAP-tag,C-type lectin domain family 4 member K
E: SNAP-tag,C-type lectin domain family 4 member K


Theoretical massNumber of molelcules
Total (without water)363,2876
Polymers363,2876
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
SNAP-tag,C-type lectin domain family 4 member K / Langerin


Mass: 60547.773 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: 185 amino acids SNAP-tag + 3xHA tag (YPYDVPDYAYPYDVPDYAYPYDVPDYA) + Linker (GSSG) + HRV3C cleavage site (LEVLFQGP)
Source: (gene. exp.) Homo sapiens (human) / Gene: CD207, CLEC4K / Cell line (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: Q9UJ71

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Repeating unit of langerin lattice in Birbeck granule / Type: COMPLEX
Details: Birbeck granules isolated from 293T cells by immunoprecipitation.
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: 293T / Plasmid: pcDNA3.1
Buffer solutionpH: 7.2
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blot for 10 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 35000 X / Nominal defocus max: 6000 nm / Nominal defocus min: 3000 nm / Calibrated defocus min: 2600 nm / Calibrated defocus max: 8500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.74 sec. / Electron dose: 1.24 e/Å2 / Avg electron dose per subtomogram: 49.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1IMOD4.11.11volume selection
2RELION4volume selection
3SerialEM3.8image acquisition
5RELION4CTF correction
8UCSF Chimera1.15model fitting
10PHENIX1.19.2model refinement
12RELION4final Euler assignment
13RELION4classification
14RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63563 / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 33 / Num. of volumes extracted: 93953
Atomic model buildingProtocol: BACKBONE TRACE
Atomic model buildingPDB-ID: 3KQG

3kqg

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