+Open data
-Basic information
Entry | Database: PDB / ID: 6v8x | |||||||||
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Title | VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure | |||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Trimer / Complex / Immunogen / HIV-1 / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / complement activation, classical pathway / host cell endosome membrane / antigen binding / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell ...immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / complement activation, classical pathway / host cell endosome membrane / antigen binding / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / blood microparticle / viral protein processing / immune response / 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 space / extracellular exosome / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
Authors | Henderson, R. / Acharya, P. | |||||||||
Funding support | United States, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6v8x.cif.gz | 552.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v8x.ent.gz | 462.4 KB | Display | PDB format |
PDBx/mmJSON format | 6v8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v8x_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 6v8x_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 6v8x_validation.xml.gz | 87.2 KB | Display | |
Data in CIF | 6v8x_validation.cif.gz | 131.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/6v8x ftp://data.pdbj.org/pub/pdb/validation_reports/v8/6v8x | HTTPS FTP |
-Related structure data
Related structure data | 21111MC 6v8zC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Envelope glycoprotein ... , 2 types, 6 molecules AEIBFJ
#1: Protein | Mass: 52791.840 Da / Num. of mol.: 3 / Fragment: UNP residues 32-502 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6 #2: Protein | Mass: 16447.670 Da / Num. of mol.: 3 / Fragment: UNP residues 519-663 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S9 |
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-Antibody , 2 types, 6 molecules CGKDHL
#3: Antibody | Mass: 24367.631 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6N095 #4: Antibody | Mass: 22930.412 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6PIL8 |
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-Sugars , 4 types, 51 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #7: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Details: unspecified | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C3 (3 fold cyclic) |
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77632 / Symmetry type: POINT |