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Yorodumi- EMDB-33548: The local map of the ternary complex of human IgM-Fc with the J c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33548 | |||||||||
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Title | The local map of the ternary complex of human IgM-Fc with the J chain and P. falciparum TM284VAR1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / P. falciparum protein / antibody / IMMUNE SYSTEM | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | 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_33548.map.gz | 230.1 MB | EMDB map data format | |
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Header (meta data) | emd-33548-v30.xml emd-33548.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_33548.png | 26.9 KB | ||
Filedesc metadata | emd-33548.cif.gz | 3.6 KB | ||
Others | emd_33548_half_map_1.map.gz emd_33548_half_map_2.map.gz | 226.8 MB 226.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33548 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33548 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33548.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33548_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33548_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 in complex with the J chain and t...
Entire | Name: Ternary complex of human IgM-Fc in complex with the J chain and the P. falciparum TM284VAR1 |
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Components |
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-Supramolecule #1: Ternary complex of human IgM-Fc in complex with the J chain and t...
Supramolecule | Name: Ternary complex of human IgM-Fc in complex with the J chain and the P. falciparum TM284VAR1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9 |
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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 |
-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: 2.0 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 59.74 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 849826 |