+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20074 | ||||||||||||
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Title | Chimpanzee SIV Env trimeric ectodomain. | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information membrane fusion involved in viral entry into host cell / host cell endosome membrane / membrane => GO:0016020 / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Simian immunodeficiency virus | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||
Authors | Pallesen J / Andrabi R / de Val N / Burton DR / Ward AB | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Cell Rep / Year: 2019 Title: The Chimpanzee SIV Envelope Trimer: Structure and Deployment as an HIV Vaccine Template. Authors: Raiees Andrabi / Jesper Pallesen / Joel D Allen / Ge Song / Jinsong Zhang / Natalia de Val / Gavin Gegg / Katelyn Porter / Ching-Yao Su / Matthias Pauthner / Amanda Newman / Hilary Bouton- ...Authors: Raiees Andrabi / Jesper Pallesen / Joel D Allen / Ge Song / Jinsong Zhang / Natalia de Val / Gavin Gegg / Katelyn Porter / Ching-Yao Su / Matthias Pauthner / Amanda Newman / Hilary Bouton-Verville / Fernando Garces / Ian A Wilson / Max Crispin / Beatrice H Hahn / Barton F Haynes / Laurent Verkoczy / Andrew B Ward / Dennis R Burton / Abstract: Epitope-targeted HIV vaccine design seeks to focus antibody responses to broadly neutralizing antibody (bnAb) sites by sequential immunization. A chimpanzee simian immunodeficiency virus (SIV) ...Epitope-targeted HIV vaccine design seeks to focus antibody responses to broadly neutralizing antibody (bnAb) sites by sequential immunization. A chimpanzee simian immunodeficiency virus (SIV) envelope (Env) shares a single bnAb site, the variable loop 2 (V2)-apex, with HIV, suggesting its possible utility in an HIV immunization strategy. Here, we generate a chimpanzee SIV Env trimer, MT145K, which displays selective binding to HIV V2-apex bnAbs and precursor versions, but no binding to other HIV specificities. We determine the structure of the MT145K trimer by cryo-EM and show that its architecture is remarkably similar to HIV Env. Immunization of an HIV V2-apex bnAb precursor Ab-expressing knockin mouse with the chimpanzee MT145K trimer induces HIV V2-specific neutralizing responses. Subsequent boosting with an HIV trimer cocktail induces responses that exhibit some virus cross-neutralization. Overall, the chimpanzee MT145K trimer behaves as expected from design both in vitro and in vivo and is an attractive potential component of a sequential immunization regimen to induce V2-apex bnAbs. | ||||||||||||
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_20074.map.gz | 78.1 MB | EMDB map data format | |
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Header (meta data) | emd-20074-v30.xml emd-20074.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20074_fsc.xml | 9.6 KB | Display | FSC data file |
Images | emd_20074.png | 162.7 KB | ||
Others | emd_20074_half_map_1.map.gz emd_20074_half_map_2.map.gz | 65.4 MB 65.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20074 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20074 | HTTPS FTP |
-Validation report
Summary document | emd_20074_validation.pdf.gz | 708.5 KB | Display | EMDB validaton report |
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Full document | emd_20074_full_validation.pdf.gz | 708 KB | Display | |
Data in XML | emd_20074_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | emd_20074_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20074 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20074 | HTTPS FTP |
-Related structure data
Related structure data | 6ohyMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20074.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.02 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_20074_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_20074_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Chimpanzee SIV Env trimeric ectodomain.
Entire | Name: Chimpanzee SIV Env trimeric ectodomain. |
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Components |
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-Supramolecule #1: Chimpanzee SIV Env trimeric ectodomain.
Supramolecule | Name: Chimpanzee SIV Env trimeric ectodomain. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Simian immunodeficiency virus |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 450 KDa |
-Macromolecule #1: Envelope glycoprotein gp160
Macromolecule | Name: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Simian immunodeficiency virus |
Molecular weight | Theoretical: 51.708664 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ENWWVTVYYG VPVWREAKTT LFCASDAKSY STEAHNIWAT QACVPTDPTP QEVLLPNVTE EFNMWENYMV DQMQEDIISL WEQSLKPCV KLTPLCVTLT CNNPTNTSCT NSTDDRLGDM RNCSFNVTTE LRDKKRKVYS LFYVEDITAI GNNSTYRLIN C NTTAITQA ...String: ENWWVTVYYG VPVWREAKTT LFCASDAKSY STEAHNIWAT QACVPTDPTP QEVLLPNVTE EFNMWENYMV DQMQEDIISL WEQSLKPCV KLTPLCVTLT CNNPTNTSCT NSTDDRLGDM RNCSFNVTTE LRDKKRKVYS LFYVEDITAI GNNSTYRLIN C NTTAITQA CPKTSFEPIP IHYCAPAGFA LLKCNDIDYK GNETCKNVST VHCTHGIKPV ATTQLILNGS TADNQTVARI DP SENLAII QLKDPVKITC RRPGNNTRGQ IQIGPAMTFY NIENVVGDTR KAYCEINGTQ WAKALNETKE VLRNILRKNI SFM VPSGGD PEVTNHHFNC GGEFFYCNTS EIINITKINK TENMTIIPCR IRQIVNSWMR VGKGIFAPPI RGNITCTSNI TGML LEIHK NREDQGEDQD QNNTYVCLTG GNMKDIWRSE LYKYKIVEIQ PLGVAPTKCR RY |
-Macromolecule #2: Envelope glycoprotein gp160
Macromolecule | Name: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Simian immunodeficiency virus |
Molecular weight | Theoretical: 17.17949 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LGALFLGFLG AAGSTMGAAS VVLTVQARQL LTGIVQQQNN LLRAPEAQQH LLQLSVWGIK QLQARVLAVE RYLRDQQLLG LWGCTGKTI CCTAVRWNKT WGNISDYQVI WNNYTWQQWD REVNNYTGLI YTLLEEANTQ QEKNEKELLE LD |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 24 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 10.0 sec. / Average electron dose: 94.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |