+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32906 | |||||||||
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Title | Structure of human langerin complex in Birbeck granules | |||||||||
Map data | Langerin trimer in the Birbeck granule. | |||||||||
Sample |
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Keywords | Birbeck granule / C-type lectin / Langerhans cell / virus defense / MEMBRANE PROTEIN | |||||||||
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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 6.4 Å | |||||||||
Authors | Oda T / Yanagisawa H | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32906.map.gz | 5.8 MB | EMDB map data format | |
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Header (meta data) | emd-32906-v30.xml emd-32906.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32906_fsc.xml | 4.6 KB | Display | FSC data file |
Images | emd_32906.png | 49.7 KB | ||
Others | emd_32906_additional_1.map.gz emd_32906_half_map_1.map.gz emd_32906_half_map_2.map.gz | 4.6 MB 5.9 MB 5.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32906 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32906 | HTTPS FTP |
-Related structure data
Related structure data | 7wz8MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32906.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Langerin trimer in the Birbeck granule. | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.67 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Langerin trimer in the Birbeck granule. The second...
File | emd_32906_additional_1.map | ||||||||||||
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Annotation | Langerin trimer in the Birbeck granule. The second body of multibody refinement. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_32906_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_32906_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Repeating unit of langerin lattice in Birbeck granule
Entire | Name: Repeating unit of langerin lattice in Birbeck granule |
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Components |
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-Supramolecule #1: Repeating unit of langerin lattice in Birbeck granule
Supramolecule | Name: 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. |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: SNAP-tag,C-type lectin domain family 4 member K
Macromolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 60.547773 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | 2D array |
-Sample preparation
Concentration | 0.05 mg/mL |
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Buffer | pH: 7.2 |
Grid | Model: 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 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 10 seconds before plunging. |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 8.5 µm / Calibrated defocus min: 2.6 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 35000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |