[English] 日本語
Yorodumi- PDB-6xrt: Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xrt | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP.664 | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM/Viral Protein / SHIV / V1V2 / V2-Apex / SOSIP / Vaccine / PGT145 / IMMUNE SYSTEM / IMMUNE SYSTEM-Viral Protein complex | |||||||||
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 / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 Macaca mulatta (Rhesus monkey) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Gorman, J. / Kwong, P.D. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Science / Year: 2021 Title: Recapitulation of HIV-1 Env-antibody coevolution in macaques leading to neutralization breadth. Authors: Ryan S Roark / Hui Li / Wilton B Williams / Hema Chug / Rosemarie D Mason / Jason Gorman / Shuyi Wang / Fang-Hua Lee / Juliette Rando / Mattia Bonsignori / Kwan-Ki Hwang / Kevin O Saunders / ...Authors: Ryan S Roark / Hui Li / Wilton B Williams / Hema Chug / Rosemarie D Mason / Jason Gorman / Shuyi Wang / Fang-Hua Lee / Juliette Rando / Mattia Bonsignori / Kwan-Ki Hwang / Kevin O Saunders / Kevin Wiehe / M Anthony Moody / Peter T Hraber / Kshitij Wagh / Elena E Giorgi / Ronnie M Russell / Frederic Bibollet-Ruche / Weimin Liu / Jesse Connell / Andrew G Smith / Julia DeVoto / Alexander I Murphy / Jessica Smith / Wenge Ding / Chengyan Zhao / Neha Chohan / Maho Okumura / Christina Rosario / Yu Ding / Emily Lindemuth / Anya M Bauer / Katharine J Bar / David Ambrozak / Cara W Chao / Gwo-Yu Chuang / Hui Geng / Bob C Lin / Mark K Louder / Richard Nguyen / Baoshan Zhang / Mark G Lewis / Donald D Raymond / Nicole A Doria-Rose / Chaim A Schramm / Daniel C Douek / Mario Roederer / Thomas B Kepler / Garnett Kelsoe / John R Mascola / Peter D Kwong / Bette T Korber / Stephen C Harrison / Barton F Haynes / Beatrice H Hahn / George M Shaw / Abstract: Neutralizing antibodies elicited by HIV-1 coevolve with viral envelope proteins (Env) in distinctive patterns, in some cases acquiring substantial breadth. We report that primary HIV-1 envelope ...Neutralizing antibodies elicited by HIV-1 coevolve with viral envelope proteins (Env) in distinctive patterns, in some cases acquiring substantial breadth. We report that primary HIV-1 envelope proteins-when expressed by simian-human immunodeficiency viruses in rhesus macaques-elicited patterns of Env-antibody coevolution very similar to those in humans, including conserved immunogenetic, structural, and chemical solutions to epitope recognition and precise Env-amino acid substitutions, insertions, and deletions leading to virus persistence. The structure of one rhesus antibody, capable of neutralizing 49% of a 208-strain panel, revealed a V2 apex mode of recognition like that of human broadly neutralizing antibodies (bNAbs) PGT145 and PCT64-35S. Another rhesus antibody bound the CD4 binding site by CD4 mimicry, mirroring human bNAbs 8ANC131, CH235, and VRC01. Virus-antibody coevolution in macaques can thus recapitulate developmental features of human bNAbs, thereby guiding HIV-1 immunogen design. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6xrt.cif.gz | 372.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6xrt.ent.gz | 319.1 KB | Display | PDB format |
PDBx/mmJSON format | 6xrt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xrt_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6xrt_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 6xrt_validation.xml.gz | 68.1 KB | Display | |
Data in CIF | 6xrt_validation.cif.gz | 97.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/6xrt ftp://data.pdbj.org/pub/pdb/validation_reports/xr/6xrt | HTTPS FTP |
-Related structure data
Related structure data | 22295MC 6xcjC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 2 types, 6 molecules GEFBCA
#1: Protein | Mass: 53300.348 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: Q2N0S6 #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: Q2N0S6 |
---|
-Antibody , 2 types, 2 molecules HL
#3: Antibody | Mass: 14704.290 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human) |
---|---|
#4: Antibody | Mass: 11312.331 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human) |
-Sugars , 6 types, 58 molecules
#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 | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 #7: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]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 #10: Sugar | ChemComp-NAG / |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||||||||
Source (natural) | Organism: Human immunodeficiency virus 1 | ||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||
Buffer component | Formula: PBS | ||||||||||||||||||
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: C-flat-1.2/1.3 | ||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 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 / C2 aperture diameter: 70 µm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 71.06 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1945 |
Image scans | Movie frames/image: 50 |
-Processing
Software | Name: PHENIX / Version: dev_3885: / Classification: refinement | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21480 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4TVP | ||||||||||||||||||||||||||||
Refine LS restraints |
|