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Yorodumi- EMDB-22498: N611-site directed response of rabbit #1 week 6 polyclonal fragme... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22498 | |||||||||||||||
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Title | N611-site directed response of rabbit #1 week 6 polyclonal fragment antigen binding in complex with 1PGE-THIVC SOSIP | |||||||||||||||
Map data | Final map | |||||||||||||||
Sample |
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Biological species | Oryctolagus cuniculus (rabbit) | |||||||||||||||
Method | single particle reconstruction / negative staining / Resolution: 29.0 Å | |||||||||||||||
Authors | Sewell LM / Ozorowski G / Ward AB | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: PLoS Pathog / Year: 2021 Title: Elicitation of potent serum neutralizing antibody responses in rabbits by immunization with an HIV-1 clade C trimeric Env derived from an Indian elite neutralizer. Authors: Rajesh Kumar / Suprit Deshpande / Leigh M Sewall / Gabriel Ozorowski / Christopher A Cottrell / Wen-Hsin Lee / Lauren G Holden / Sara T Richey / Antra Singh Chandrawacar / Kanika Dhiman / ...Authors: Rajesh Kumar / Suprit Deshpande / Leigh M Sewall / Gabriel Ozorowski / Christopher A Cottrell / Wen-Hsin Lee / Lauren G Holden / Sara T Richey / Antra Singh Chandrawacar / Kanika Dhiman / Ashish / Vivek Kumar / Shubbir Ahmed / Nitin Hingankar / Naresh Kumar / Kailapuri G Murugavel / Aylur K Srikrishnan / Devin Sok / Andrew B Ward / Jayanta Bhattacharya / Abstract: Evaluating the structure-function relationship of viral envelope (Env) evolution and the development of broadly cross-neutralizing antibodies (bnAbs) in natural infection can inform rational ...Evaluating the structure-function relationship of viral envelope (Env) evolution and the development of broadly cross-neutralizing antibodies (bnAbs) in natural infection can inform rational immunogen design. In the present study, we examined the magnitude and specificity of autologous neutralizing antibodies induced in rabbits by a novel HIV-1 clade C Env protein (1PGE-THIVC) vis-à-vis those developed in an elite neutralizer from whom the env sequence was obtained that was used to prepare the soluble Env protein. The novel 1PGE-THIVC Env trimer displayed a native like pre-fusion closed conformation in solution as determined by small angle X-ray scattering (SAXS) and negative stain electron microscopy (EM). This closed spike conformation of 1PGE-THIVC Env trimers was correlated with weak or undetectable binding of non-neutralizing monoclonal antibodies (mAbs) compared to neutralizing mAbs. Furthermore, 1PGE-THIVC SOSIP induced potent neutralizing antibodies in rabbits to autologous virus variants. The autologous neutralizing antibody specificity induced in rabbits by 1PGE-THIVC was mapped to the C3/V4 region (T362/P401) of viral Env. This observation agreed with electron microscopy polyclonal epitope mapping (EMPEM) of the Env trimer complexed with IgG Fab prepared from the immunized rabbit sera. Our study demonstrated neutralization of sequence matched and unmatched autologous viruses by serum antibodies induced in rabbits by 1PGE-THIVC and also highlighted a comparable specificity for the 1PGE-THIVC SOSIP trimer with that seen with polyclonal antibodies elicited in the elite neutralizer by negative-stain electron microscopy polyclonal epitope (ns-EMPEM) mapping. | |||||||||||||||
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_22498.map.gz | 8.9 MB | EMDB map data format | |
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Header (meta data) | emd-22498-v30.xml emd-22498.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | emd_22498.png | 61 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22498 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22498 | HTTPS FTP |
-Validation report
Summary document | emd_22498_validation.pdf.gz | 288.9 KB | Display | EMDB validaton report |
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Full document | emd_22498_full_validation.pdf.gz | 288.5 KB | Display | |
Data in XML | emd_22498_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | emd_22498_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22498 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22498 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22498.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Final map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.98 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 : N611-site directed response of rabbit #1 week 6 polyclonal fragme...
Entire | Name: N611-site directed response of rabbit #1 week 6 polyclonal fragment antigen binding in complex with 1PGE-THIVC SOSIP |
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Components |
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-Supramolecule #1: N611-site directed response of rabbit #1 week 6 polyclonal fragme...
Supramolecule | Name: N611-site directed response of rabbit #1 week 6 polyclonal fragment antigen binding in complex with 1PGE-THIVC SOSIP type: complex / ID: 1 / Parent: 0 Details: IgG was purified from rabbit serum and digested into Fab using papain. Polyclonal fab was incubated with 1PGE-THIVC SOSIP trimers. |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Staining | Type: NEGATIVE / Material: Uranyl formate / Details: 2% UF, stained once for 30-60 s prior to blotting | |||||||||
Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: PARLODION / Support film - #0 - topology: CONTINUOUS / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING |
-Electron microscopy
Microscope | TFS TALOS F200C |
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Image recording | Film or detector model: FEI CETA (4k x 4k) / Average exposure time: 1.0 sec. / 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 magnification: 73000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |