+Open data
-Basic information
Entry | Database: PDB / ID: 6nij | ||||||||||||||||||
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Title | PGT145 Fab in complex with full length AMC011 HIV-1 Env | ||||||||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV-1 / antibody / glycoprotein | ||||||||||||||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.7 Å | ||||||||||||||||||
Authors | Cottrell, C.A. / Torrents de la Pena, A. / Rantalainen, K. / Torres, J.L. / Ward, A.B. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: PLoS Pathog / Year: 2019 Title: Similarities and differences between native HIV-1 envelope glycoprotein trimers and stabilized soluble trimer mimetics. Authors: Alba Torrents de la Peña / Kimmo Rantalainen / Christopher A Cottrell / Joel D Allen / Marit J van Gils / Jonathan L Torres / Max Crispin / Rogier W Sanders / Andrew B Ward / Abstract: The HIV-1 envelope glycoprotein (Env) trimer is located on the surface of the virus and is the target of broadly neutralizing antibodies (bNAbs). Recombinant native-like soluble Env trimer mimetics, ...The HIV-1 envelope glycoprotein (Env) trimer is located on the surface of the virus and is the target of broadly neutralizing antibodies (bNAbs). Recombinant native-like soluble Env trimer mimetics, such as SOSIP trimers, have taken a central role in HIV-1 vaccine research aimed at inducing bNAbs. We therefore performed a direct and thorough comparison of a full-length unmodified Env trimer containing the transmembrane domain and the cytoplasmic tail, with the sequence matched soluble SOSIP trimer, both based on an early Env sequence (AMC011) from an HIV+ individual that developed bNAbs. The structures of the full-length AMC011 trimer bound to either bNAb PGT145 or PGT151 were very similar to the structures of SOSIP trimers. Antigenically, the full-length and SOSIP trimers were comparable, but in contrast to the full-length trimer, the SOSIP trimer did not bind at all to non-neutralizing antibodies, most likely as a consequence of the intrinsic stabilization of the SOSIP trimer. Furthermore, the glycan composition of full-length and SOSIP trimers was similar overall, but the SOSIP trimer possessed slightly less complex and less extensively processed glycans, which may relate to the intrinsic stabilization as well as the absence of the membrane tether. These data provide insights into how to best use and improve membrane-associated full-length and soluble SOSIP HIV-1 Env trimers as immunogens. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6nij.cif.gz | 402.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nij.ent.gz | 327.3 KB | Display | PDB format |
PDBx/mmJSON format | 6nij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nij_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6nij_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6nij_validation.xml.gz | 57.4 KB | Display | |
Data in CIF | 6nij_validation.cif.gz | 86.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/6nij ftp://data.pdbj.org/pub/pdb/validation_reports/ni/6nij | HTTPS FTP |
-Related structure data
Related structure data | 9378MC 6olpC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-AMC011 Glycoprotein ... , 2 types, 6 molecules ACEBDF
#3: Protein | Mass: 52880.039 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) #4: Protein | Mass: 39677.762 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) |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 15550.196 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 12350.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
-Sugars , 3 types, 7 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 |
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#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: Sugar | ChemComp-NAG / |
-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 | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / 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 |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||
3D reconstruction | Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51588 / Symmetry type: POINT | ||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |