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- EMDB-32906: Structure of human langerin complex in Birbeck granules -

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Basic information

Entry
Database: EMDB / ID: EMD-32906
TitleStructure of human langerin complex in Birbeck granules
Map dataLangerin trimer in the Birbeck granule.
Sample
  • Complex: Repeating unit of langerin lattice in Birbeck granule
    • Protein or peptide: SNAP-tag,C-type lectin domain family 4 member K
KeywordsBirbeck granule / C-type lectin / Langerhans cell / virus defense / MEMBRANE PROTEIN
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / pattern recognition receptor activity / D-mannose binding / endocytic vesicle / clathrin-coated endocytic vesicle membrane / carbohydrate binding / early endosome membrane / defense response to virus / immune response / 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)
Methodsubtomogram averaging / cryo EM / Resolution: 6.4 Å
AuthorsOda T / Yanagisawa H
Funding support Japan, 1 items
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, 2022-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32906.png

Downloads & links

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Map

FileDownload / File: emd_32906.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLangerin trimer in the Birbeck granule.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.67 Å/pix.
x 128 pix.
= 341.76 Å		2.67 Å/pix.
x 128 pix.
= 341.76 Å		2.67 Å/pix.
x 128 pix.
= 341.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.93
Minimum - Maximum-2.1185644 - 9.347019
Average (Standard dev.)0.120605834 (±0.33453304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 341.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Langerin trimer in the Birbeck granule. The second...

Fileemd_32906_additional_1.map
AnnotationLangerin trimer in the Birbeck granule. The second body of multibody refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_32906_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_32906_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Repeating unit of langerin lattice in Birbeck granule

EntireName: Repeating unit of langerin lattice in Birbeck granule
Components
  • Complex: Repeating unit of langerin lattice in Birbeck granule
    • Protein or peptide: SNAP-tag,C-type lectin domain family 4 member K

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Supramolecule #1: Repeating unit of langerin lattice in Birbeck granule

SupramoleculeName: Repeating unit of langerin lattice in Birbeck granule / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Birbeck granules isolated from 293T cells by immunoprecipitation.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: SNAP-tag,C-type lectin domain family 4 member K

MacromoleculeName: SNAP-tag,C-type lectin domain family 4 member K / type: protein_or_peptide / ID: 1
Details: 185 amino acids SNAP-tag + 3xHA tag (YPYDVPDYAYPYDVPDYAYPYDVPDYA) + Linker (GSSG) + HRV3C cleavage site (LEVLFQGP)
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.547773 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDKDCEMKRT TLDSPLGKLE LSGCEQGLHE IKLLGKGTSA ADAVEVPAPA AVLGGPEPLM QATAWLNAYF HQPEAIEEFP VPALHHPVF QQESFTRQVL WKLLKVVKFG EVISYQQLAA LAGNPAATAA VKTALSGNPV PILIPCHRVV SSSGAVGGYE G GLAVKEWL ...String:
MDKDCEMKRT TLDSPLGKLE LSGCEQGLHE IKLLGKGTSA ADAVEVPAPA AVLGGPEPLM QATAWLNAYF HQPEAIEEFP VPALHHPVF QQESFTRQVL WKLLKVVKFG EVISYQQLAA LAGNPAATAA VKTALSGNPV PILIPCHRVV SSSGAVGGYE G GLAVKEWL LAHEGHRLGK PGLGPAGYPY DVPDYAYPYD VPDYAYPYDV PDYAGSSGLE VLFQGPTVEK EAPDAHFTVD KQ NISLWPR EPPPKSGPSL VPGKTPTVRA ALICLTLVLV ASVLLQAVLY PRFMGTISDV KTNVQLLKGR VDNISTLDSE IKK NSDGME AAGVQIQMVN ESLGYVRSQF LKLKTSVEKA NAQIQILTRS WEEVSTLNAQ IPELKSDLEK ASALNTKIRA LQGS LENMS KLLKRQNDIL QVVSQGWKYF KGNFYYFSLI PKTWYSAEQF CVSRNSHLTS VTSESEQEFL YKTAGGLIYW IGLTK AGME GDWSWVDDTP FNKVQSARFW IPGEPNNAGN NEHCGNIKAP SLQAWNDAPC DKTFLFICKR PYVPSEP

UniProtKB: C-type lectin domain family 4 member K

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state2D array

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 7.2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 10 seconds before plunging.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 0.74 sec. / Average electron dose: 1.24 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 8.5 µm / Calibrated defocus min: 2.6 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 35000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 63563
ExtractionNumber tomograms: 33 / Number images used: 93953 / Software: (Name: IMOD (ver. 4.11.11), RELION (ver. 4.0))
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3kqg


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: BACKBONE TRACE
Output model

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

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