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Yorodumi- EMDB-21112: VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Str... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21112 | |||||||||
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Title | VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure | |||||||||
Map data | VRC03 and 10-1074 Bound BG505 F14/Vt8 HIV-1 SOSIP Envelope Trimer | |||||||||
Sample |
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Keywords | Trimer / Complex / Immunogen / HIV-1 / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information immunoglobulin complex / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response ...immunoglobulin complex / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Henderson R / Acharya P / Bartesaghi A / Zhou Y | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements. Authors: Rory Henderson / Maolin Lu / Ye Zhou / Zekun Mu / Robert Parks / Qifeng Han / Allen L Hsu / Elizabeth Carter / Scott C Blanchard / R J Edwards / Kevin Wiehe / Kevin O Saunders / Mario J ...Authors: Rory Henderson / Maolin Lu / Ye Zhou / Zekun Mu / Robert Parks / Qifeng Han / Allen L Hsu / Elizabeth Carter / Scott C Blanchard / R J Edwards / Kevin Wiehe / Kevin O Saunders / Mario J Borgnia / Alberto Bartesaghi / Walther Mothes / Barton F Haynes / Priyamvada Acharya / S Munir Alam / Abstract: The trimeric HIV-1 Envelope protein (Env) mediates viral-host cell fusion via a network of conformational transitions, with allosteric elements in each protomer orchestrating host receptor-induced ...The trimeric HIV-1 Envelope protein (Env) mediates viral-host cell fusion via a network of conformational transitions, with allosteric elements in each protomer orchestrating host receptor-induced exposure of the co-receptor binding site and fusion elements. To understand the molecular details of this allostery, here, we introduce Env mutations aimed to prevent CD4-induced rearrangements in the HIV-1 BG505 Env trimer. Binding analysis and single-molecule Förster Resonance Energy Transfer confirm that these mutations prevent CD4-induced transitions of the HIV-1 Env. Structural analysis by single-particle cryo-electron microscopy performed on the BG505 SOSIP mutant Env proteins shows rearrangements in the gp120 topological layer contacts with gp41. Displacement of a conserved tryptophan (W571) from its typical pocket in these Env mutants renders the Env insensitive to CD4 binding. These results reveal the critical function of W571 as a conformational switch in Env allostery and receptor-mediated viral entry and provide insights on Env conformation that are relevant for vaccine design. | |||||||||
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_21112.map.gz | 43 MB | EMDB map data format | |
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Header (meta data) | emd-21112-v30.xml emd-21112.xml | 18.9 KB 18.9 KB | Display Display | EMDB header |
Images | emd_21112.png | 44.3 KB | ||
Filedesc metadata | emd-21112.cif.gz | 6.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21112 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21112 | HTTPS FTP |
-Validation report
Summary document | emd_21112_validation.pdf.gz | 674 KB | Display | EMDB validaton report |
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Full document | emd_21112_full_validation.pdf.gz | 673.5 KB | Display | |
Data in XML | emd_21112_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_21112_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21112 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21112 | HTTPS FTP |
-Related structure data
Related structure data | 6v8zMC 6v8xC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21112.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | VRC03 and 10-1074 Bound BG505 F14/Vt8 HIV-1 SOSIP Envelope Trimer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08312 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 between VRC03, 10-1074, and BG505 F14 HIV-1 SOSIP Env Trimer
+Supramolecule #1: Complex between VRC03, 10-1074, and BG505 F14 HIV-1 SOSIP Env Trimer
+Supramolecule #2: BG505 F14/Vt8 HIV-1 SOSIP Env Trimer
+Supramolecule #3: VRC03
+Supramolecule #4: 10-1074
+Macromolecule #1: Envelope glycoprotein gp120
+Macromolecule #2: envelope glycoprotein gp41
+Macromolecule #3: 10-1074 Fab Heavy Chain
+Macromolecule #4: 10-1074 Fab Light Chain
+Macromolecule #5: VRC03 Fab Heavy Chain
+Macromolecule #6: VRC03 Fab Light Chain
+Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84378 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |