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Yorodumi- PDB-8tni: Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with bro... -
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-Basic information
Entry | Database: PDB / ID: 8tni | ||||||
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Title | Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing bi-specific antibody CAP256L-R27 targeting the CD4-binding site and the V2-apex | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 Envelope / bi-specific / antibody / nanobody / VHH / llama / BG505 DS-SOSIP / neutralization / CAP256 / R27 / immunization / 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.61 Å | ||||||
Authors | Zhou, T. / Morano, N.C. / Roark, R.S. / Kwong, P.D. / Xu, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing bi-specific antibody CAP256L-R27 targeting the CD4-binding site and the V2-apex Authors: Xu, J. / Zhou, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tni.cif.gz | 447.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tni.ent.gz | 364 KB | Display | PDB format |
PDBx/mmJSON format | 8tni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/8tni ftp://data.pdbj.org/pub/pdb/validation_reports/tn/8tni | HTTPS FTP |
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-Related structure data
Related structure data | 41417MC 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
-HIV-1 BG505 DS-SOSIP ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 54086.324 Da / Num. of mol.: 3 / Fragment: UNP residues 30-505 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6 #2: Protein | Mass: 17146.482 Da / Num. of mol.: 3 / Fragment: UNP residues 509-661 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6 |
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-Antibody , 2 types, 4 molecules HIJX
#3: Antibody | Mass: 36949.734 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293F / Production host: Homo sapiens (human) #4: Antibody | | Mass: 26863.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293F / Production host: Homo sapiens (human) |
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-Sugars , 4 types, 49 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 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 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: Complex between HIV-1 Env BG505 DS-SOSIP and Bi-specific antibody CAP256L-R27 Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.405 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK 293F / Plasmid: pVRC8400 |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Purified complex by FPLC and concentrated to final concentration. |
Vitrification | Cryogen name: ETHANE |
-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 FIELDBright-field microscopy / Nominal magnification: 103000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 70 K |
Image recording | Electron dose: 58.06 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1189143 / Details: Blob pick in cryoSparc | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.61 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 236154 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | B value: 82.9 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7LPN Accession code: 7LPN / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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