+
Open data
-
Basic information
Entry | Database: PDB / ID: 8s2e | ||||||
---|---|---|---|---|---|---|---|
Title | Fab4251-DS-SOSIP complex | ||||||
![]() |
| ||||||
![]() | VIRAL PROTEIN / HIV | ||||||
Biological species | ![]() HIV whole-genome vector AA1305#18 (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
![]() | Nortier, P. / Perez, L. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: RAIN: a Machine Learning-based identification for HIV-1 bNAbs. Authors: Laurent Perez / Mathilde Foglierini / ![]() Abstract: Broadly neutralizing antibodies (bNAbs) are promising candidates for the treatment and prevention of HIV-1 infection. Despite their critical importance, automatic detection of HIV-1 bNAbs from immune ...Broadly neutralizing antibodies (bNAbs) are promising candidates for the treatment and prevention of HIV-1 infection. Despite their critical importance, automatic detection of HIV-1 bNAbs from immune repertoire is still lacking. Here, we developed a straightforward computational method for apid utomatic dentification of bAbs ) based on Machine Learning methods. In contrast to other approaches using one-hot encoding amino acid sequences or structural alignment for prediction, RAIN uses a combination of selected sequence-based features for accurate prediction of HIV-1 bNAbs. We demonstrate the performance of our approach on non-biased, experimentally obtained sequenced BCR repertoires from HIV-1 immune donors. RAIN processing leads to the successful identification of novel HIV-1 bNAbs targeting the CD4-binding site of the envelope glycoprotein. In addition, we validate the identified bNAbs using neutralization assay and we solve the structure of one of them in complex with the soluble native-like heterotrimeric envelope glycoprotein by single-particle cryo-electron microscopy (cryo-EM). Overall, we propose a method to facilitate and accelerate HIV-1 bNAbs discovery from non-selected immune repertoires. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 367.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 65.6 KB | Display | |
Data in CIF | ![]() | 98.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Envelope glycoprotein ... , 2 types, 6 molecules AECBDF
#3: Protein | Mass: 49558.484 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Envelope glycoprotein gp120|Human immunodeficiency virus 1 Source: (gene. exp.) HIV whole-genome vector AA1305#18 (others) Production host: ![]() #4: Protein | Mass: 14561.529 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV whole-genome vector AA1305#18 (others) Production host: ![]() |
---|
-Antibody / Protein , 2 types, 2 molecules HL
#1: Antibody | Mass: 23951.986 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Protein | Mass: 22257.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 4 types, 45 molecules ![](data/chem/img/NAG.gif)
#5: 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 #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Envelope glycoprotein Human immunodeficiency virus 1 with Fab Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 400 kDa/nm / Experimental value: NO |
Source (natural) | Organism: HIV whole-genome vector AA1305#18 (others) |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 6 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 80 % |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: OTHER / Nominal magnification: 165000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 39.89 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 15163 |
-
Processing
EM software | Name: cryoSPARC / Category: 3D reconstruction | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72497 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
|