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Yorodumi- EMDB-21327: Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex w... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21327 | ||||||||||||
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Title | Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and two copies of PGZL1 Fab | ||||||||||||
Map data | Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and two copies of PGZL1 Fab | ||||||||||||
Sample |
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Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.6 Å | ||||||||||||
Authors | Rantalainen K / Lee WS / 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_21327.map.gz | 116.4 MB | EMDB map data format | |
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Header (meta data) | emd-21327-v30.xml emd-21327.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21327_fsc.xml | 11.5 KB | Display | FSC data file |
Images | emd_21327.png | 152.4 KB | ||
Others | emd_21327_half_map_1.map.gz emd_21327_half_map_2.map.gz | 98.3 MB 98.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21327 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21327 | HTTPS FTP |
-Validation report
Summary document | emd_21327_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_21327_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_21327_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21327 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21327 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21327.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and two copies of PGZL1 Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half-map 1
File | emd_21327_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_21327_half_map_2.map | ||||||||||||
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Annotation | half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex w...
Entire | Name: Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and two copies of PGZL1 Fab |
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Components |
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-Supramolecule #1: Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex w...
Supramolecule | Name: Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and two copies of PGZL1 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11 Details: AMC011 Env purified with stabilizing PGT151 Fab. Complexed with PGZL1 Fab during detergent-lipid exchange and prior to grid preparation. |
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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 | 5.6 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
Details | AMC011 Env purified with stabilizing PGT151 Fab. Complexed with PGZL1 Fab during detergent-lipid exchange and prior to grid preparation. Sample is in detergent-lipid micelle. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 5788 / Average electron dose: 50.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |