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Yorodumi- EMDB-6372: JRFL Env SOSIP.664 in complex with CD4-binding site broadly neutr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6372 | |||||||||
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Title | JRFL Env SOSIP.664 in complex with CD4-binding site broadly neutralizing antibody DRVIA7 | |||||||||
Map data | HIV-1 soluble Env SOSIP trimer in complex with broadly neutralizing antibody DRVIA7 Fab | |||||||||
Sample |
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Keywords | HIV-1 / Env / broadly-neutralizing antibody / CD4 binding site / SOSIP | |||||||||
Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 21.0 Å | |||||||||
Authors | Ozorowski G / Ward AB | |||||||||
Citation | Journal: Immunity / Year: 2016 Title: Key gp120 Glycans Pose Roadblocks to the Rapid Development of VRC01-Class Antibodies in an HIV-1-Infected Chinese Donor. Authors: Leopold Kong / Bin Ju / Yajing Chen / Linling He / Li Ren / Jiandong Liu / Kunxue Hong / Bin Su / Zheng Wang / Gabriel Ozorowski / Xiaolin Ji / Yuanzi Hua / Yanli Chen / Marc C Deller / ...Authors: Leopold Kong / Bin Ju / Yajing Chen / Linling He / Li Ren / Jiandong Liu / Kunxue Hong / Bin Su / Zheng Wang / Gabriel Ozorowski / Xiaolin Ji / Yuanzi Hua / Yanli Chen / Marc C Deller / Yanling Hao / Yi Feng / Fernando Garces / Richard Wilson / Kaifan Dai / Sijy O'Dell / Krisha McKee / John R Mascola / Andrew B Ward / Richard T Wyatt / Yuxing Li / Ian A Wilson / Jiang Zhu / Yiming Shao / Abstract: VRC01-class antibodies neutralize diverse HIV-1 strains by targeting the conserved CD4-binding site. Despite extensive investigations, crucial events in the early stage of VRC01 development remain ...VRC01-class antibodies neutralize diverse HIV-1 strains by targeting the conserved CD4-binding site. Despite extensive investigations, crucial events in the early stage of VRC01 development remain elusive. We demonstrated how VRC01-class antibodies emerged in a Chinese donor by antigen-specific single B cell sorting, structural and functional studies, and longitudinal antibody and virus repertoire analyses. A monoclonal antibody DRVIA7 with modest neutralizing breadth was isolated that displayed a subset of VRC01 signatures. X-ray and EM structures revealed a VRC01-like angle of approach, but less favorable interactions between the DRVIA7 light-chain CDR1 and the N terminus with N276 and V5 glycans of gp120. Although the DRVIA7 lineage was unable to acquire broad neutralization, longitudinal analysis revealed a repertoire-encoded VRC01 light-chain CDR3 signature and VRC01-like neutralizing heavy-chain precursors that rapidly matured within 2 years. Thus, light chain accommodation of the glycan shield should be taken into account in vaccine design targeting this conserved site of vulnerability. | |||||||||
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_6372.map.gz | 14.5 MB | EMDB map data format | |
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Header (meta data) | emd-6372-v30.xml emd-6372.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
Images | emd_6372.png | 60.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6372 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6372 | HTTPS FTP |
-Validation report
Summary document | emd_6372_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
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Full document | emd_6372_full_validation.pdf.gz | 77.1 KB | Display | |
Data in XML | emd_6372_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6372 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6372 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6372.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | HIV-1 soluble Env SOSIP trimer in complex with broadly neutralizing antibody DRVIA7 Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Fab of broadly neutralizing antibody DRVIA7 in complex with HIV-1...
Entire | Name: Fab of broadly neutralizing antibody DRVIA7 in complex with HIV-1 JRFL Env SOSIP.664 trimer |
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Components |
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-Supramolecule #1000: Fab of broadly neutralizing antibody DRVIA7 in complex with HIV-1...
Supramolecule | Name: Fab of broadly neutralizing antibody DRVIA7 in complex with HIV-1 JRFL Env SOSIP.664 trimer type: sample / ID: 1000 Details: Incubated Fab with trimer overnight at room temperature prior to placing on grid. Oligomeric state: Trimer of JRFL SOSIP.664 with one Fab bound to each protomer Number unique components: 2 |
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Molecular weight | Theoretical: 570 KDa |
-Macromolecule #1: HIV-1 Env SOSIP gp140
Macromolecule | Name: HIV-1 Env SOSIP gp140 / type: protein_or_peptide / ID: 1 / Name.synonym: SOSIP.664 / Number of copies: 1 / Oligomeric state: Trimer / Recombinant expression: Yes |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: JRFL / synonym: HIV-1 |
Molecular weight | Theoretical: 420 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F |
-Macromolecule #2: DRVIA7 anti-HIV antibody Fab
Macromolecule | Name: DRVIA7 anti-HIV antibody Fab / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 50 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 mg/mL |
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Buffer | pH: 7.4 / Details: 50 mM Tris-HCl, pH 7.4, 150 mM NaCl |
Staining | Type: NEGATIVE Details: Grids containing adsorbed protein were treated with 3 uL of 2% w/v uranyl formate for 60 seconds. Uranyl formate was then removed with blotting paper. |
Grid | Details: Glow-discharged CU400 copper grids with carbon support |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | OTHER |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 73,000 magnification. |
Specialist optics | Energy filter - Name: FEI |
Details | A series of tilts from 0 to 50 degrees in 10 degree increments was collected to increase side views. |
Date | Apr 6, 2015 |
Image recording | Category: CCD / Film or detector model: FEI CETA (4k x 4k) / Number real images: 142 / Average electron dose: 25.05 e/Å2 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -1.5 µm / Nominal defocus min: -1.5 µm / Nominal magnification: 73000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle min: -50 |
-Image processing
Details | Particles were selected automatically using DogPicker. Initial 2D class averages were inspected; those displaying complexes of trimer with Fab were subjected another round of classification. Only classes that clearly showed two or three Fabs per trimer were used for reconstruction. |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: OTHER / Software - Name: EMAN2, Sparx / Number images used: 10685 |