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Yorodumi- EMDB-33539: Cryo-EM local structure of human IgM-Fc in complex with the J cha... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33539 | |||||||||
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Title | Cryo-EM local structure of human IgM-Fc in complex with the J chain and the DBL domain of DBLMSP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | malaria / immunoglobin / DBLMSP / IMMUNE SYSTEM | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.64 Å | |||||||||
Authors | Shen H / Ji C / Xiao J | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Plasmodium falciparum has evolved multiple mechanisms to hijack human immunoglobulin M Authors: Ji C / Shen H / Su C / Li Y / Chen S / Sharp TH / Xiao J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33539.map.gz | 118.1 MB | EMDB map data format | |
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Header (meta data) | emd-33539-v30.xml emd-33539.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_33539.png | 39 KB | ||
Filedesc metadata | emd-33539.cif.gz | 3.7 KB | ||
Others | emd_33539_half_map_1.map.gz emd_33539_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33539 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33539 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33539.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33539_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33539_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of human IgM-Fc with the J chain and the DBL doma...
Entire | Name: Ternary complex of human IgM-Fc with the J chain and the DBL domain of DBLMSP |
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Components |
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-Supramolecule #1: Ternary complex of human IgM-Fc with the J chain and the DBL doma...
Supramolecule | Name: Ternary complex of human IgM-Fc with the J chain and the DBL domain of DBLMSP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10 |
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Source (natural) | Organism: Plasmodium falciparum (malaria parasite P. falciparum) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 391618 |