+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9003 | |||||||||
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Title | CP506 Fab/BG505 SOSIP.664 complexe | |||||||||
Map data | CP506 Fab/BG505 SOSIP.664 complexes | |||||||||
Sample |
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Biological species | Cavia porcellus (domestic guinea pig) / Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 26.5 Å | |||||||||
Authors | Yang YY / Ward AB | |||||||||
Citation | Journal: Cell Rep / Year: 2019 Title: The HIV-1 Envelope Glycoprotein C3/V4 Region Defines a Prevalent Neutralization Epitope following Immunization. Authors: Lin Lei / Yuhe R Yang / Karen Tran / Yimeng Wang / Chi-I Chiang / Gabriel Ozorowski / Yongli Xiao / Andrew B Ward / Richard T Wyatt / Yuxing Li / Abstract: Despite recent progress in engineering native trimeric HIV-1 envelope glycoprotein (Env) mimics as vaccine candidates, Env trimers often induce vaccine-matched neutralizing antibody (NAb) responses. ...Despite recent progress in engineering native trimeric HIV-1 envelope glycoprotein (Env) mimics as vaccine candidates, Env trimers often induce vaccine-matched neutralizing antibody (NAb) responses. Understanding the specificities of autologous NAb responses and the underlying molecular mechanisms restricting the neutralization breadth is therefore informative to improve vaccine efficacy. Here, we delineate the response specificity by single B cell sorting and serum analysis of guinea pigs immunized with BG505 SOSIP.664 Env trimers. Our results reveal a prominent immune target containing both conserved and strain-specific residues in the C3/V4 region of Env in trimer-vaccinated animals. The defined NAb response shares a high degree of similarity with the early NAb response developed by a naturally infected infant from whom the HIV virus strain BG505 was isolated and later developed a broadly NAb response. Our study describes strain-specific responses and their possible evolution pathways, thereby highlighting the potential to broaden NAb responses by immunogen re-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_9003.map.gz | 20.6 MB | EMDB map data format | |
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Header (meta data) | emd-9003-v30.xml emd-9003.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9003_fsc.xml | 8.1 KB | Display | FSC data file |
Images | emd_9003.png | 52.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9003 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9003 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9003.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CP506 Fab/BG505 SOSIP.664 complexes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.05 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 : CP506 Fab/BG505 SOSIP.664 complex
Entire | Name: CP506 Fab/BG505 SOSIP.664 complex |
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Components |
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-Supramolecule #1: CP506 Fab/BG505 SOSIP.664 complex
Supramolecule | Name: CP506 Fab/BG505 SOSIP.664 complex / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Cavia porcellus (domestic guinea pig) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #2: BG505 SOSIP.664 Env trimer
Supramolecule | Name: BG505 SOSIP.664 Env trimer / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: guinea pig CP506 Fab
Supramolecule | Name: guinea pig CP506 Fab / type: complex / ID: 3 / Parent: 2 |
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Source (natural) | Organism: Cavia porcellus (domestic guinea pig) |
Recombinant expression | Organism: Homo sapiens (human) |
-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 |
Staining | Type: NEGATIVE / Material: 2% Uranyl Formate |
Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus min: 1.5 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average exposure time: 0.5 sec. / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |