+Open data
-Basic information
Entry | Database: PDB / ID: 7t9b | |||||||||||||||
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Title | ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs | |||||||||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / HIV / germline targeting vaccine / 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 / 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 / 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) Mus musculus (house mouse) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.72 Å | |||||||||||||||
Authors | Berndsen, Z.T. / Ward, A.B. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Immunity / Year: 2022 Title: Priming HIV Envelope V2 Apex-directed broadly neutralizing antibody responses with protein or mRNA immunogens Authors: Melzi, E. / Willis, J. / Ma, K. / Lin, Y. / Kratochvil, S. / Berndsen, Z.T. / Nair, U. / Warner, J. / Steichen, J. / Pecetta, S. / Perez, M. / Kirsch, K. / Ward, A.B. / Schief, W. / Batista, F.D. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t9b.cif.gz | 541.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t9b.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7t9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t9b_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 7t9b_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 7t9b_validation.xml.gz | 85.5 KB | Display | |
Data in CIF | 7t9b_validation.cif.gz | 129.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/7t9b ftp://data.pdbj.org/pub/pdb/validation_reports/t9/7t9b | HTTPS FTP |
-Related structure data
Related structure data | 25755MC 7t9aC 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 Envelope ApexGT5 ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 53196.496 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): HEK / Production host: Homo sapiens (human) #2: Protein | Mass: 17134.324 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6 |
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-Antibody , 4 types, 8 molecules JMOKNPHL
#3: Antibody | Mass: 13511.111 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK / Production host: Homo sapiens (human) #4: Antibody | Mass: 13508.800 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK / Production host: Homo sapiens (human) #5: Antibody | | Mass: 15126.627 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK / Production host: Homo sapiens (human) #6: Antibody | | Mass: 11605.943 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK / Production host: Homo sapiens (human) |
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-Sugars , 7 types, 63 molecules
#7: 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 #8: Polysaccharide | #9: Polysaccharide | Source method: isolated from a genetically manipulated source #10: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #11: Polysaccharide | Source method: isolated from a genetically manipulated source #12: Polysaccharide | Source method: isolated from a genetically manipulated source #13: 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: HIV-1 Envelope ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35763 / Symmetry type: POINT |