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Yorodumi- EMDB-23778: Negative stain EM map of BG505 SOSIP in complex with Rh4O9.8 mono... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23778 | |||||||||
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Title | Negative stain EM map of BG505 SOSIP in complex with Rh4O9.8 monoclonal antibody (as Fab fragment) | |||||||||
Map data | 3D map of BG505 SOSIP in complex with the monoclonal antibody Rh4O9.8 (as Fab fragment). Obtained by negative stain EM. | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 15.9 Å | |||||||||
Authors | Antanasijevic A / Ward AB | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Sci Adv / Year: 2022 Title: From structure to sequence: Antibody discovery using cryoEM. Authors: Aleksandar Antanasijevic / Charles A Bowman / Robert N Kirchdoerfer / Christopher A Cottrell / Gabriel Ozorowski / Amit A Upadhyay / Kimberly M Cirelli / Diane G Carnathan / Chiamaka A ...Authors: Aleksandar Antanasijevic / Charles A Bowman / Robert N Kirchdoerfer / Christopher A Cottrell / Gabriel Ozorowski / Amit A Upadhyay / Kimberly M Cirelli / Diane G Carnathan / Chiamaka A Enemuo / Leigh M Sewall / Bartek Nogal / Fangzhu Zhao / Bettina Groschel / William R Schief / Devin Sok / Guido Silvestri / Shane Crotty / Steven E Bosinger / Andrew B Ward / Abstract: One of the rate-limiting steps in analyzing immune responses to vaccines or infections is the isolation and characterization of monoclonal antibodies. Here, we present a hybrid structural and ...One of the rate-limiting steps in analyzing immune responses to vaccines or infections is the isolation and characterization of monoclonal antibodies. Here, we present a hybrid structural and bioinformatic approach to directly assign the heavy and light chains, identify complementarity-determining regions, and discover sequences from cryoEM density maps of serum-derived polyclonal antibodies bound to an antigen. When combined with next-generation sequencing of immune repertoires, we were able to specifically identify clonal family members, synthesize the monoclonal antibodies, and confirm that they interact with the antigen in a manner equivalent to the corresponding polyclonal antibodies. This structure-based approach for identification of monoclonal antibodies from polyclonal sera opens new avenues for analysis of immune responses and iterative vaccine design. | |||||||||
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_23778.map.gz | 32.9 MB | EMDB map data format | |
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Header (meta data) | emd-23778-v30.xml emd-23778.xml | 13 KB 13 KB | Display Display | EMDB header |
Images | emd_23778.png | 50.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23778 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23778 | HTTPS FTP |
-Validation report
Summary document | emd_23778_validation.pdf.gz | 300.9 KB | Display | EMDB validaton report |
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Full document | emd_23778_full_validation.pdf.gz | 300.5 KB | Display | |
Data in XML | emd_23778_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_23778_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23778 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23778 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23778.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D map of BG505 SOSIP in complex with the monoclonal antibody Rh4O9.8 (as Fab fragment). Obtained by negative stain EM. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.77 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 : BG505 SOSIP.v5.2 in complex with the monoclonal antibody Rh4O9.8 ...
Entire | Name: BG505 SOSIP.v5.2 in complex with the monoclonal antibody Rh4O9.8 (as Fab fragment) |
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Components |
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-Supramolecule #1: BG505 SOSIP.v5.2 in complex with the monoclonal antibody Rh4O9.8 ...
Supramolecule | Name: BG505 SOSIP.v5.2 in complex with the monoclonal antibody Rh4O9.8 (as Fab fragment) type: complex / ID: 1 / Parent: 0 Details: Fab fragment was generated by proteolytic cleavage of IgG antibody |
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Source (natural) | Organism: Human immunodeficiency virus |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pPPI4 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: TBS, 0.2um filtered | |||||||||
Staining | Type: NEGATIVE / Material: Uranyl formate / Details: The samples were stained with UF for 60s. | |||||||||
Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Details | The complex was generated by incubation of Rh4O9.8 monoclonal antibody (as Fab) with recombinantly expressed BG505 SOSIP and subsequent SEC purification. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |