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Yorodumi- EMDB-21344: Complex of HIV-1 Envelope glycoprotein clone BG505-ST-710 and 10E... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21344 | ||||||||||||
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Title | Complex of HIV-1 Envelope glycoprotein clone BG505-ST-710 and 10E8 Fab in DOPC-DOPS-CHS peptidisc | ||||||||||||
Map data | Complex of HIV-1 Envelope glycoprotein clone BG505-ST-710 and 10E8 Fab in DOPC-DOPS-CHS peptidisc | ||||||||||||
Sample |
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Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | ||||||||||||
Authors | Rantalainen K / Ward ABW | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Cell Rep / Year: 2020 Title: HIV-1 Envelope and MPER Antibody Structures in Lipid Assemblies. Authors: Kimmo Rantalainen / Zachary T Berndsen / Aleksandar Antanasijevic / Torben Schiffner / Xi Zhang / Wen-Hsin Lee / Jonathan L Torres / Lei Zhang / Adriana Irimia / Jeffrey Copps / Kenneth H ...Authors: Kimmo Rantalainen / Zachary T Berndsen / Aleksandar Antanasijevic / Torben Schiffner / Xi Zhang / Wen-Hsin Lee / Jonathan L Torres / Lei Zhang / Adriana Irimia / Jeffrey Copps / Kenneth H Zhou / Young D Kwon / William H Law / Chaim A Schramm / Raffaello Verardi / Shelly J Krebs / Peter D Kwong / Nicole A Doria-Rose / Ian A Wilson / Michael B Zwick / John R Yates / William R Schief / Andrew B Ward / Abstract: Structural and functional studies of HIV envelope glycoprotein (Env) as a transmembrane protein have long been complicated by challenges associated with inherent flexibility of the molecule and the ...Structural and functional studies of HIV envelope glycoprotein (Env) as a transmembrane protein have long been complicated by challenges associated with inherent flexibility of the molecule and the membrane-embedded hydrophobic regions. Here, we present approaches for incorporating full-length, wild-type HIV-1 Env, as well as C-terminally truncated and stabilized versions, into lipid assemblies, providing a modular platform for Env structural studies by single particle electron microscopy. We reconstitute a full-length Env clone into a nanodisc, complex it with a membrane-proximal external region (MPER) targeting antibody 10E8, and structurally define the full quaternary epitope of 10E8 consisting of lipid, MPER, and ectodomain contacts. By aligning this and other Env-MPER antibody complex reconstructions with the lipid bilayer, we observe evidence of Env tilting as part of the neutralization mechanism for MPER-targeting antibodies. We also adapt the platform toward vaccine design purposes by introducing stabilizing mutations that allow purification of unliganded Env with a peptidisc scaffold. | ||||||||||||
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_21344.map.gz | 79.3 MB | EMDB map data format | |
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Header (meta data) | emd-21344-v30.xml emd-21344.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_21344.png | 63.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21344 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21344 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21344.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Complex of HIV-1 Envelope glycoprotein clone BG505-ST-710 and 10E8 Fab in DOPC-DOPS-CHS peptidisc | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Complex of HIV-1 Envelope glycoprotein clone BG505-ST-710 and 10E...
Entire | Name: Complex of HIV-1 Envelope glycoprotein clone BG505-ST-710 and 10E8 Fab in DOPC-DOPS-CHS peptidisc |
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Components |
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-Supramolecule #1: Complex of HIV-1 Envelope glycoprotein clone BG505-ST-710 and 10E...
Supramolecule | Name: Complex of HIV-1 Envelope glycoprotein clone BG505-ST-710 and 10E8 Fab in DOPC-DOPS-CHS peptidisc type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11 |
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Source (natural) | Organism: Homo sapiens (human) |
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 | 0.05 mg/mL |
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Buffer | pH: 7.4 |
Staining | Type: NEGATIVE / Material: Uranyl formate |
Grid | Details: unspecified |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Detector mode: COUNTING / Number real images: 403 / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 52392 |
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CTF correction | Software - Name: Gctf (ver. 1.06) |
Startup model | Type of model: OTHER / Details: Ab-initio model generated in cryoSPARC2 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2) |
Final 3D classification | Software - Name: cryoSPARC (ver. 2) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 17567 |