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Yorodumi- PDB-7ur6: Cryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ur6 | |||||||||
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Title | Cryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561.DH1021.14 in complex with stabilized HIV-1 Env Ce1176 DS-SOSIP.664 | |||||||||
Components |
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Keywords | VIRAL PROTEIN/Immune System / FP / HIV-1 / SOSIP / Vaccine / IMMUNE SYSTEM / Rhesus / SHIV / VIRAL PROTEIN / VIRAL PROTEIN-Immune System 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 ...: / 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 / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 Macaca mulatta (Rhesus monkey) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å | |||||||||
Authors | Gorman, J. / Kwong, P.D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Cryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561.DH1021.14 in complex with stabilized HIV-1 Env Ce1176 DS-SOSIP.664 Authors: Gorman, J. / Kwong, P.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ur6.cif.gz | 480.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ur6.ent.gz | 407.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ur6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ur6_validation.pdf.gz | 3.6 MB | Display | wwPDB validaton report |
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Full document | 7ur6_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 7ur6_validation.xml.gz | 75.8 KB | Display | |
Data in CIF | 7ur6_validation.cif.gz | 114.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/7ur6 ftp://data.pdbj.org/pub/pdb/validation_reports/ur/7ur6 | HTTPS FTP |
-Related structure data
Related structure data | 26706MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 6 molecules GAFBCI
#1: Protein | Mass: 53648.887 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: C6G0D7 #2: Protein | Mass: 17240.510 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: C6G0E7 |
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-Antibody , 2 types, 6 molecules HDJLEK
#3: Antibody | Mass: 14505.475 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human) #4: Antibody | Mass: 11679.873 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human) |
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-Sugars , 6 types, 84 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 | Source method: isolated from a genetically manipulated source #8: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Polysaccharide | Source method: isolated from a genetically manipulated source #10: 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 | Name: Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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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 | Conc.: 1 X / Name: PBS / 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 |
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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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 70 µm |
Image recording | Average exposure time: 2 sec. / Electron dose: 51.27 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 |
-Processing
Software | Name: PHENIX / Version: 1.20_4459: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13272 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 6VTT | ||||||||||||||||||||||||
Refine LS restraints |
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