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Yorodumi- EMDB-8299: AMC011 HIV-1 Env SOSIP trimer in complex with autologous anti-HIV... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8299 | |||||||||
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Title | AMC011 HIV-1 Env SOSIP trimer in complex with autologous anti-HIV antibody ACS202 | |||||||||
Map data | AMC011 HIV-1 Env SOSIP trimer in complex with anti-HIV antibody ACS202 | |||||||||
Sample |
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Biological species | Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 21.0 Å | |||||||||
Authors | Ozorowski G / Ward AB | |||||||||
Citation | Journal: Nat Microbiol / Year: 2016 Title: An HIV-1 antibody from an elite neutralizer implicates the fusion peptide as a site of vulnerability. Authors: Marit J van Gils / Tom L G M van den Kerkhof / Gabriel Ozorowski / Christopher A Cottrell / Devin Sok / Matthias Pauthner / Jesper Pallesen / Natalia de Val / Anila Yasmeen / Steven W de ...Authors: Marit J van Gils / Tom L G M van den Kerkhof / Gabriel Ozorowski / Christopher A Cottrell / Devin Sok / Matthias Pauthner / Jesper Pallesen / Natalia de Val / Anila Yasmeen / Steven W de Taeye / Anna Schorcht / Stephanie Gumbs / Inez Johanna / Karen Saye-Francisco / Chi-Hui Liang / Elise Landais / Xiaoyan Nie / Laura K Pritchard / Max Crispin / Garnett Kelsoe / Ian A Wilson / Hanneke Schuitemaker / Per Johan Klasse / John P Moore / Dennis R Burton / Andrew B Ward / Rogier W Sanders / Abstract: The induction by vaccination of broadly neutralizing antibodies (bNAbs) capable of neutralizing various HIV-1 viral strains is challenging, but understanding how a subset of HIV-infected individuals ...The induction by vaccination of broadly neutralizing antibodies (bNAbs) capable of neutralizing various HIV-1 viral strains is challenging, but understanding how a subset of HIV-infected individuals develops bNAbs may guide immunization strategies. Here, we describe the isolation and characterization of the bNAb ACS202 from an elite neutralizer that recognizes a new, trimer-specific and cleavage-dependent epitope at the gp120-gp41 interface of the envelope glycoprotein (Env), involving the glycan N88 and the gp41 fusion peptide. In addition, an Env trimer, AMC011 SOSIP.v4.2, based on early virus isolates from the same elite neutralizer, was constructed, and its structure by cryo-electron microscopy at 6.2 Å resolution reveals a closed, pre-fusion conformation similar to that of the BG505 SOSIP.664 trimer. The availability of a native-like Env trimer and a bNAb from the same elite neutralizer provides the opportunity to design vaccination strategies aimed at generating similar bNAbs against a key functional site on HIV-1. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8299.map.gz | 13.7 MB | EMDB map data format | |
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Header (meta data) | emd-8299-v30.xml emd-8299.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_8299.png | 68.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8299 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8299 | HTTPS FTP |
-Validation report
Summary document | emd_8299_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_8299_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_8299_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8299 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8299 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8299.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | AMC011 HIV-1 Env SOSIP trimer in complex with anti-HIV antibody ACS202 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : AMC011 HIV-1 Env trimer in complex with three copies of anti-HIV ...
Entire | Name: AMC011 HIV-1 Env trimer in complex with three copies of anti-HIV antibody ACS202 fragment antigen binding |
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Components |
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-Supramolecule #1: AMC011 HIV-1 Env trimer in complex with three copies of anti-HIV ...
Supramolecule | Name: AMC011 HIV-1 Env trimer in complex with three copies of anti-HIV antibody ACS202 fragment antigen binding type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: AMC011 |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pPPI4 |
Molecular weight | Theoretical: 570 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 7.4 / Details: Tris-buffered saline |
Staining | Type: NEGATIVE / Material: uranyl formate Details: Negatively stained with 2% w/v uranyl formate for 60 seconds. |
Grid | Model: EMS Cu400 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER |
Details | The two components of the complex were incubated overnight at room temperature (molar excess of Fab) and diluted prior to grid preparation. |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI CETA (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Average electron dose: 25.0 e/Å2 Details: Stage tilt of -50, -40, -30, -20, -10, 0 degrees to increase orientation sampling |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 73000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |