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Yorodumi- EMDB-3067: cryoEM reconstruction of 3BC315 Fab in complex with BG505 SOSIP.6... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3067 | |||||||||
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Title | cryoEM reconstruction of 3BC315 Fab in complex with BG505 SOSIP.664 Env trimer | |||||||||
Map data | Reconstruction of 3BC315 Fab bound to BG505 SOSIP.664 | |||||||||
Sample |
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Keywords | HIV-1 / Env / SOSIP / bnAb / broadly neutralizing antibody / 3BC315 | |||||||||
Biological species | Human Immunodeficiency Virus-1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.3 Å | |||||||||
Authors | Lee JH / Ward AB | |||||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Antibodies to a conformational epitope on gp41 neutralize HIV-1 by destabilizing the Env spike. Authors: Jeong Hyun Lee / Daniel P Leaman / Arthur S Kim / Alba Torrents de la Peña / Kwinten Sliepen / Anila Yasmeen / Ronald Derking / Alejandra Ramos / Steven W de Taeye / Gabriel Ozorowski / ...Authors: Jeong Hyun Lee / Daniel P Leaman / Arthur S Kim / Alba Torrents de la Peña / Kwinten Sliepen / Anila Yasmeen / Ronald Derking / Alejandra Ramos / Steven W de Taeye / Gabriel Ozorowski / Florian Klein / Dennis R Burton / Michel C Nussenzweig / Pascal Poignard / John P Moore / Per Johan Klasse / Rogier W Sanders / Michael B Zwick / Ian A Wilson / Andrew B Ward / Abstract: The recent identification of three broadly neutralizing antibodies (bnAbs) against gp120-gp41 interface epitopes has expanded the targetable surface on the HIV-1 envelope glycoprotein (Env) trimer. ...The recent identification of three broadly neutralizing antibodies (bnAbs) against gp120-gp41 interface epitopes has expanded the targetable surface on the HIV-1 envelope glycoprotein (Env) trimer. By using biochemical, biophysical and computational methods, we map the previously unknown trimer epitopes of two related antibodies, 3BC315 and 3BC176. A cryo-EM reconstruction of a soluble Env trimer bound to 3BC315 Fab at 9.3 Å resolution reveals that the antibody binds between two gp41 protomers, and neutralizes the virus by accelerating trimer decay. In contrast, bnAb 35O22 binding to a partially overlapping quaternary epitope at the gp120-gp41 interface does not induce decay. A conserved gp41-proximal glycan at N88 was also shown to play a role in the binding kinetics of 3BC176 and 3BC315. Finally, our data suggest that the dynamic structure of the Env trimer influences exposure of bnAb epitopes. | |||||||||
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_3067.map.gz | 38.7 MB | EMDB map data format | |
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Header (meta data) | emd-3067-v30.xml emd-3067.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | emd_3067.png | 401.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3067 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3067 | HTTPS FTP |
-Validation report
Summary document | emd_3067_validation.pdf.gz | 230 KB | Display | EMDB validaton report |
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Full document | emd_3067_full_validation.pdf.gz | 229.2 KB | Display | |
Data in XML | emd_3067_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3067 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3067 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3067.map.gz / Format: CCP4 / Size: 41.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of 3BC315 Fab bound to BG505 SOSIP.664 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.21 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 : 3BC315 Fab in complex with BG505 SOSIP.664 trimer
Entire | Name: 3BC315 Fab in complex with BG505 SOSIP.664 trimer |
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Components |
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-Supramolecule #1000: 3BC315 Fab in complex with BG505 SOSIP.664 trimer
Supramolecule | Name: 3BC315 Fab in complex with BG505 SOSIP.664 trimer / type: sample / ID: 1000 / Oligomeric state: Two 3BC315 Fabs bind one SOSIP.664 trimer / Number unique components: 2 |
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Molecular weight | Theoretical: 520 KDa |
-Macromolecule #1: HIV-1 Envelope glycoprotein
Macromolecule | Name: HIV-1 Envelope glycoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: BG505 SOSIP.664 Details: BG505 Env trimer ectodomain with the SOSIP mutations and truncation at residue 664 Number of copies: 1 / Oligomeric state: trimer / Recombinant expression: Yes |
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Source (natural) | Organism: Human Immunodeficiency Virus-1 / Strain: BG505 / synonym: HIV-1 |
Molecular weight | Theoretical: 420 KDa |
Recombinant expression | Organism: Mammalian (mammals) / Recombinant cell: HEK293F / Recombinant plasmid: pPPI4 |
-Macromolecule #2: 3BC315 Antibody Fab
Macromolecule | Name: 3BC315 Antibody Fab / type: protein_or_peptide / ID: 2 / Name.synonym: 3BC315 Fab / Details: Each Fab is a LC-HC heterodimer. / Number of copies: 2 / Oligomeric state: heterodimer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 500 KDa |
Recombinant expression | Organism: Mammalian (mammals) / Recombinant cell: HEK293F |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.4 / Details: 20 mM Tris 150 mM NaCl |
Grid | Details: 400 mesh Cu grid with holey carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: HOMEMADE PLUNGER Method: DDM added to the sample prior to freezing, to final concentration of 0.003% (w/v) |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism corrected at 50,000x mag |
Date | Jan 9, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 2393 / Average electron dose: 27 e/Å2 Details: Every image is an average of 25 frames recorded by the direct electron detector. |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Whole micrograph |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: OTHER / Software - Name: Relion Details: Frames 5-25 were used for the final particle reconstruction, due to large frame shifts in the first 4 frames. Number images used: 20252 |