+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6333 | |||||||||
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Title | Structure of DEC205 at acidic pH | |||||||||
Map data | Reconstruction of DEC205 at acidic pH | |||||||||
Sample |
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Keywords | dendritic cell receptor / apoptosis / cryoEM / mannose receptor family | |||||||||
Function / homology | Function and homology information endocytosis / signaling receptor activity / carbohydrate binding / inflammatory response / immune response / external side of plasma membrane / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 14.6 Å | |||||||||
Authors | Cao L / Shi X / Chang H / Zhang Q / Wah C / He Y | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2015 Title: pH-Dependent recognition of apoptotic and necrotic cells by the human dendritic cell receptor DEC205. Authors: Longxing Cao / Xiangyi Shi / Haishuang Chang / Qinfen Zhang / Yongning He / Abstract: Dendritic cells play important roles in regulating innate and adaptive immune responses. DEC205 (CD205) is one of the major endocytotic receptors on dendritic cells and has been widely used for ...Dendritic cells play important roles in regulating innate and adaptive immune responses. DEC205 (CD205) is one of the major endocytotic receptors on dendritic cells and has been widely used for vaccine generation against viruses and tumors. However, little is known about its structure and functional mechanism. Here we determine the structure of the human DEC205 ectodomain by cryoelectron microscopy. The structure shows that the 12 extracellular domains form a compact double ring-shaped conformation at acidic pH and become extended at basic pH. Biochemical data indicate that the pH-dependent conformational change of DEC205 is correlated with ligand binding and release. DEC205 only binds to apoptotic and necrotic cells at acidic pH, whereas live cells cannot be recognized by DEC205 at either acidic or basic conditions. These results suggest that DEC205 is an immune receptor that recognizes apoptotic and necrotic cells specifically through a pH-dependent mechanism. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6333.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-6333-v30.xml emd-6333.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | 400_6333.gif 80_6333.gif | 42.7 KB 3.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6333 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6333 | HTTPS FTP |
-Validation report
Summary document | emd_6333_validation.pdf.gz | 79.3 KB | Display | EMDB validaton report |
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Full document | emd_6333_full_validation.pdf.gz | 78.4 KB | Display | |
Data in XML | emd_6333_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6333 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6333 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6333.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of DEC205 at acidic pH | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : DEC205 ectodomain at pH 6.0
Entire | Name: DEC205 ectodomain at pH 6.0 |
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Components |
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-Supramolecule #1000: DEC205 ectodomain at pH 6.0
Supramolecule | Name: DEC205 ectodomain at pH 6.0 / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1 |
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Molecular weight | Theoretical: 191.2 MDa |
-Macromolecule #1: CD205, Lymphocyte antigen 75
Macromolecule | Name: CD205, Lymphocyte antigen 75 / type: protein_or_peptide / ID: 1 / Name.synonym: DEC205 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: Plasma membrane |
Molecular weight | Theoretical: 191.2 MDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: Human / Recombinant cell: HEK293 / Recombinant plasmid: pTT5 |
Sequence | UniProtKB: Lymphocyte antigen 75 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.0 mg/mL |
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Buffer | pH: 6 / Details: 150mM NaCl, 50mM Bis-Tris |
Staining | Type: NEGATIVE / Details: Cryo |
Grid | Details: Quantifoil Holey Carbon Film |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: FEI VITROBOT MARK II / Method: Blot for 6 seconds before plunging |
-Electron microscopy
Microscope | JEOL 2100F |
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Specialist optics | Energy filter - Name: in column filter |
Date | Apr 1, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 153 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 11029 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 4.2 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder model: JEOL |
-Image processing
CTF correction | Details: whole micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.6 Å / Resolution method: OTHER / Software - Name: EMAN, EMAN2 / Number images used: 15723 |
Final two d classification | Number classes: 20 |