+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33438 | |||||||||||||||
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Title | Structure of the human IgM B cell receptor | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.0 Å | |||||||||||||||
Authors | Chen MY / Su Q / Shi YG | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: Science Title: Cryo-EM structure of the human IgM B cell receptor Authors: Su Q / Chen M / Shi Y | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33438.map.gz | 167.7 MB | EMDB map data format | |
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Header (meta data) | emd-33438-v30.xml emd-33438.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_33438.png | 37.6 KB | ||
Others | emd_33438_half_map_1.map.gz emd_33438_half_map_2.map.gz | 164.8 MB 164.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33438 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33438 | HTTPS FTP |
-Validation report
Summary document | emd_33438_validation.pdf.gz | 624.8 KB | Display | EMDB validaton report |
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Full document | emd_33438_full_validation.pdf.gz | 624.3 KB | Display | |
Data in XML | emd_33438_validation.xml.gz | 15 KB | Display | |
Data in CIF | emd_33438_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33438 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33438 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33438.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.077 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33438_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33438_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : structure of human B-cell antigen receptor of the IgM isotype
Entire | Name: structure of human B-cell antigen receptor of the IgM isotype |
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Components |
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-Supramolecule #1: structure of human B-cell antigen receptor of the IgM isotype
Supramolecule | Name: structure of human B-cell antigen receptor of the IgM isotype type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293 |
-Supramolecule #2: Heavy chain
Supramolecule | Name: Heavy chain / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293 |
-Supramolecule #3: Light chain
Supramolecule | Name: Light chain / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293 |
-Supramolecule #4: human B-cell antigen receptor
Supramolecule | Name: human B-cell antigen receptor / type: complex / Chimera: Yes / ID: 4 / Parent: 1 / Macromolecule list: #3-#4 |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 172330 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 172330 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |