[English] 日本語
Yorodumi- PDB-6crq: Glutaraldehyde-treated BG505 SOSIP.664 Env in complex with PGV04 Fab -
+Open data
-Basic information
Entry | Database: PDB / ID: 6crq | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Glutaraldehyde-treated BG505 SOSIP.664 Env in complex with PGV04 Fab | |||||||||||||||
Components |
| |||||||||||||||
Keywords | VIRAL PROTEIN / glutaraldehyde / BG505 / SOSIP / PGV04 / HIV / HIV-1 / trimer / immmune complex / immunogen / Env / cross link / B cell activation / Th cell activation | |||||||||||||||
Function / homology | Function and homology information 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 / 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 ...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 / 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 / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||
Authors | Pallesen, J. / Ward, A.B. | |||||||||||||||
Funding support | United States, 4items
| |||||||||||||||
Citation | Journal: PLoS Pathog / Year: 2018 Title: Structural and immunologic correlates of chemically stabilized HIV-1 envelope glycoproteins. Authors: Torben Schiffner / Jesper Pallesen / Rebecca A Russell / Jonathan Dodd / Natalia de Val / Celia C LaBranche / David Montefiori / Georgia D Tomaras / Xiaoying Shen / Scarlett L Harris / Amin ...Authors: Torben Schiffner / Jesper Pallesen / Rebecca A Russell / Jonathan Dodd / Natalia de Val / Celia C LaBranche / David Montefiori / Georgia D Tomaras / Xiaoying Shen / Scarlett L Harris / Amin E Moghaddam / Oleksandr Kalyuzhniy / Rogier W Sanders / Laura E McCoy / John P Moore / Andrew B Ward / Quentin J Sattentau / Abstract: Inducing broad spectrum neutralizing antibodies against challenging pathogens such as HIV-1 is a major vaccine design goal, but may be hindered by conformational instability within viral envelope ...Inducing broad spectrum neutralizing antibodies against challenging pathogens such as HIV-1 is a major vaccine design goal, but may be hindered by conformational instability within viral envelope glycoproteins (Env). Chemical cross-linking is widely used for vaccine antigen stabilization, but how this process affects structure, antigenicity and immunogenicity is poorly understood and its use remains entirely empirical. We have solved the first cryo-EM structure of a cross-linked vaccine antigen. The 4.2 Å structure of HIV-1 BG505 SOSIP soluble recombinant Env in complex with a CD4 binding site-specific broadly neutralizing antibody (bNAb) Fab fragment reveals how cross-linking affects key properties of the trimer. We observed density corresponding to highly specific glutaraldehyde (GLA) cross-links between gp120 monomers at the trimer apex and between gp120 and gp41 at the trimer interface that had strikingly little impact on overall trimer conformation, but critically enhanced trimer stability and improved Env antigenicity. Cross-links were also observed within gp120 at sites associated with the N241/N289 glycan hole that locally modified trimer antigenicity. In immunogenicity studies, the neutralizing antibody response to cross-linked trimers showed modest but significantly greater breadth against a global panel of difficult-to-neutralize Tier-2 heterologous viruses. Moreover, the specificity of autologous Tier-2 neutralization was modified away from the N241/N289 glycan hole, implying a novel specificity. Finally, we have investigated for the first time T helper cell responses to next-generation soluble trimers, and report on vaccine-relevant immunodominant responses to epitopes within BG505 that are modified by cross-linking. Elucidation of the structural correlates of a cross-linked viral glycoprotein will allow more rational use of this methodology for vaccine design, and reveals a strategy with promise for eliciting neutralizing antibodies needed for an effective HIV-1 vaccine. | |||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6crq.cif.gz | 519.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6crq.ent.gz | 433.7 KB | Display | PDB format |
PDBx/mmJSON format | 6crq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6crq_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6crq_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 6crq_validation.xml.gz | 77.2 KB | Display | |
Data in CIF | 6crq_validation.cif.gz | 117.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/6crq ftp://data.pdbj.org/pub/pdb/validation_reports/cr/6crq | HTTPS FTP |
-Related structure data
Related structure data | 7568MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Envelope glycoprotein ... , 2 types, 6 molecules ABFCGH
#1: Protein | Mass: 53950.172 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S5 #2: Protein | Mass: 17146.482 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S7 |
---|
-Antibody , 2 types, 6 molecules DIJEKL
#3: Antibody | Mass: 24644.771 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Antibody | Mass: 23073.822 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
---|
-Sugars , 5 types, 54 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 | Source method: isolated from a genetically manipulated source #8: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Sugar | ChemComp-NAG / |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Glutaraldehyde-treated BG505 SOSIP.664 Env in complex with PGV04 Fab Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.55 MDa / Experimental value: NO |
Source (natural) | Organism: Human immunodeficiency virus 1 |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 / Details: 50 mM Tris, 150 mM NaCl, 0.3 mM DDM. |
Buffer component | Name: TBS |
Specimen | Conc.: 1.67 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 / Nominal magnification: 29000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 7 sec. / Electron dose: 66 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1329 |
Image scans | Sampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 35 / Used frames/image: 1-35 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55563 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL |