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Yorodumi- PDB-8t2f: BG505 Boost2 SOSIP.664 in complex with NHP polyclonal antibody N289 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8t2f | ||||||||||||
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Title | BG505 Boost2 SOSIP.664 in complex with NHP polyclonal antibody N289 | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN / HIV-1 / Env / NHP / Antibody / Fusion Peptide / Polyclonal | ||||||||||||
Biological species | Human immunodeficiency virus 1 Macaca mulatta (Rhesus monkey) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Pratap, P.P. / Antansijevic, A. / Ozorowski, G. / Ward, A.B. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Focusing antibody responses to the fusion peptide in rhesus macaques Authors: Cottrell, C.A. / Pratap, P.P. / Ward, A.B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t2f.cif.gz | 625.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t2f.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8t2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8t2f_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8t2f_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8t2f_validation.xml.gz | 64.1 KB | Display | |
Data in CIF | 8t2f_validation.cif.gz | 96 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/8t2f ftp://data.pdbj.org/pub/pdb/validation_reports/t2/8t2f | HTTPS FTP |
-Related structure data
Related structure data | 40982MC 8swvC 8swwC 8t2eC M: map data used to model this data C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 8 molecules AEFBCDHL
#1: Protein | Mass: 58090.172 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human) #2: Protein | Mass: 17192.574 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human) #3: Protein | | Mass: 9890.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Macaca mulatta (Rhesus monkey) #4: Protein | | Mass: 8954.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Macaca mulatta (Rhesus monkey) |
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-Sugars , 3 types, 48 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: 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 | Value: 0.470 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 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 magnification: 22500 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 41.3591843915 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7339 |
-Processing
EM software |
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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: 75994 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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