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- EMDB-9359: Cryo-EM structure of vaccine-elicited antibody 0PV-c.01 in comple... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9359 | |||||||||
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Title | Cryo-EM structure of vaccine-elicited antibody 0PV-c.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122 | |||||||||
![]() | primary map | |||||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Gorman J / Kwong PD | |||||||||
![]() | ![]() Title: Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization. Authors: Rui Kong / Hongying Duan / Zizhang Sheng / Kai Xu / Priyamvada Acharya / Xuejun Chen / Cheng Cheng / Adam S Dingens / Jason Gorman / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / ...Authors: Rui Kong / Hongying Duan / Zizhang Sheng / Kai Xu / Priyamvada Acharya / Xuejun Chen / Cheng Cheng / Adam S Dingens / Jason Gorman / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou / Gwo-Yu Chuang / Cara W Chao / Ying Gu / Alexander J Jafari / Mark K Louder / Sijy O'Dell / Ariana P Rowshan / Elise G Viox / Yiran Wang / Chang W Choi / Martin M Corcoran / Angela R Corrigan / Venkata P Dandey / Edward T Eng / Hui Geng / Kathryn E Foulds / Yicheng Guo / Young D Kwon / Bob Lin / Kevin Liu / Rosemarie D Mason / Martha C Nason / Tiffany Y Ohr / Li Ou / Reda Rawi / Edward K Sarfo / Arne Schön / John P Todd / Shuishu Wang / Hui Wei / Winston Wu / / James C Mullikin / Robert T Bailer / Nicole A Doria-Rose / Gunilla B Karlsson Hedestam / Diana G Scorpio / Julie Overbaugh / Jesse D Bloom / Bridget Carragher / Clinton S Potter / Lawrence Shapiro / Peter D Kwong / John R Mascola / ![]() ![]() Abstract: The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be ...The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be elicited, we identified, characterized, and tracked five neutralizing Ab lineages targeting the HIV-1-fusion peptide (FP) in vaccinated macaques over time. Genetic and structural analyses revealed two of these lineages to belong to a reproducible class capable of neutralizing up to 59% of 208 diverse viral strains. B cell analysis indicated each of the five lineages to have been initiated and expanded by FP-carrier priming, with envelope (Env)-trimer boosts inducing cross-reactive neutralization. These Abs had binding-energy hotspots focused on FP, whereas several FP-directed Abs induced by immunization with Env trimer-only were less FP-focused and less broadly neutralizing. Priming with a conserved subregion, such as FP, can thus induce Abs with binding-energy hotspots coincident with the target subregion and capable of broad neutralization. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 229.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 32.6 KB 32.6 KB | Display Display | ![]() |
Images | ![]() | 144.4 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Others | ![]() ![]() ![]() | 121 MB 226.4 MB 226.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nf2MC ![]() 8977C ![]() 9189C ![]() 9319C ![]() 9320C ![]() 6mpgC ![]() 6mphC ![]() 6mqcC ![]() 6mqeC ![]() 6mqmC ![]() 6mqrC ![]() 6mqsC ![]() 6n16C ![]() 6n1vC ![]() 6n1wC ![]() 6osyC ![]() 6ot1C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07325 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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-Additional map: additional map
File | emd_9359_additional.map | ||||||||||||
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Annotation | additional map | ||||||||||||
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Density Histograms |
-Half map: half-map 1
File | emd_9359_half_map_1.map | ||||||||||||
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Annotation | half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map 2
File | emd_9359_half_map_2.map | ||||||||||||
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Annotation | half-map 2 | ||||||||||||
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Density Histograms |
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Sample components
+Entire : HIV-1 Env BG505 DS-SOSIP and antibodies 0PV-c.01, VRC03 and PGT122
+Supramolecule #1: HIV-1 Env BG505 DS-SOSIP and antibodies 0PV-c.01, VRC03 and PGT122
+Supramolecule #2: Envelope glycoprotein gp120
+Supramolecule #3: Envelope glycoprotein gp41
+Supramolecule #4: VRC03
+Supramolecule #5: PGT122
+Supramolecule #6: 0PV-c.01
+Macromolecule #1: Envelope glycoprotein gp120
+Macromolecule #2: Envelope glycoprotein gp41
+Macromolecule #3: VRC03 Heavy Chain
+Macromolecule #4: VRC03 Light Chain
+Macromolecule #5: PGT122 Heavy Chain
+Macromolecule #6: PGT122 Light Chain
+Macromolecule #7: 0PV-c.01 Heavy Chain
+Macromolecule #8: 0PV-c.01 Light Chain
+Macromolecule #16: 2-acetamido-2-deoxy-beta-D-glucopyranose
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.4 / Component - Formula: PBS |
Grid | Material: COPPER / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1767 / Average exposure time: 10.0 sec. / Average electron dose: 73.46 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
CTF correction | Software - Name: CTFFIND (ver. 4) |
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Initial angle assignment | Type: NOT APPLICABLE |
Final 3D classification | Software - Name: cryoSPARC (ver. 2) |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic![]() |