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Yorodumi- EMDB-21330: Ectodomain from nanodisc of C-terminally truncated HIV-1 Envelope... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21330 | ||||||||||||
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Title | Ectodomain from nanodisc of C-terminally truncated HIV-1 Envelope glycoprotein clone BG505 in complex with PGT151 Fab | ||||||||||||
Map data | Ectodomain from nanodisc of C-terminally truncated HIV-1 Envelope glycoprotein clone BG505 in complex with PGT151 Fab | ||||||||||||
Sample |
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Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 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_21330.map.gz | 5.9 MB | EMDB map data format | |
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Header (meta data) | emd-21330-v30.xml emd-21330.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21330_fsc.xml | 14.6 KB | Display | FSC data file |
Images | emd_21330.png | 82.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21330 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21330 | HTTPS FTP |
-Validation report
Summary document | emd_21330_validation.pdf.gz | 77.7 KB | Display | EMDB validaton report |
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Full document | emd_21330_full_validation.pdf.gz | 76.8 KB | Display | |
Data in XML | emd_21330_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21330 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21330 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21330.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Ectodomain from nanodisc of C-terminally truncated HIV-1 Envelope glycoprotein clone BG505 in complex with PGT151 Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 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 : Ectodomain from nanodisc of C-terminally truncated HIV-1 Envelope...
Entire | Name: Ectodomain from nanodisc of C-terminally truncated HIV-1 Envelope glycoprotein clone BG505 in complex with PGT151 Fab |
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Components |
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-Supramolecule #1: Ectodomain from nanodisc of C-terminally truncated HIV-1 Envelope...
Supramolecule | Name: Ectodomain from nanodisc of C-terminally truncated HIV-1 Envelope glycoprotein clone BG505 in complex with PGT151 Fab 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 | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.18 mg/mL |
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Buffer | pH: 7.4 |
Grid | Support film - Material: CARBON / Support film - topology: CONTINUOUS / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
Details | C-terminally truncated Env purified with stabilizing PGT151 Fab. Assembled to DOPC+CHS nanodisc with MSP1D1 scaffold by detergent removal with biobeads. |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Number real images: 2343 / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |