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Yorodumi- EMDB-6445: Atomic structure of a non-enveloped virus reveals pH sensors for ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6445 | |||||||||
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Title | Atomic structure of a non-enveloped virus reveals pH sensors for a coordinated process of cell entry | |||||||||
Map data | The whole map of BTV virion at pH 3.4 without imposing a reverse B-factor to boost high frequency signals | |||||||||
Sample |
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Keywords | Non-enveloped virus / cell entry / cryo-EM / pH sensor | |||||||||
Biological species | Bluetongue virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Zhang X / Patel A / Celma C / Roy P / Zhou ZH | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2016 Title: Atomic model of a nonenveloped virus reveals pH sensors for a coordinated process of cell entry. Authors: Xing Zhang / Avnish Patel / Cristina C Celma / Xuekui Yu / Polly Roy / Z Hong Zhou / Abstract: Viruses sense environmental cues such as pH to engage in membrane interactions for cell entry during infection, but how nonenveloped viruses sense pH is largely undefined. Here, we report both high- ...Viruses sense environmental cues such as pH to engage in membrane interactions for cell entry during infection, but how nonenveloped viruses sense pH is largely undefined. Here, we report both high- and low-pH structures of bluetongue virus (BTV), which enters cells via a two-stage endosomal process. The receptor-binding protein VP2 possesses a zinc finger that may function to maintain VP2 in a metastable state and a conserved His866, which senses early-endosomal pH. The membrane-penetration protein VP5 has three domains: dagger, unfurling and anchoring. Notably, the β-meander motif of the anchoring domain contains a histidine cluster that can sense late-endosomal pH and also possesses four putative membrane-interaction elements. Exposing BTV to low pH detaches VP2 and dramatically refolds the dagger and unfurling domains of VP5. Our biochemical and structure-guided-mutagenesis studies support these coordinated pH-sensing mechanisms. | |||||||||
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_6445.map.gz | 117.7 MB | EMDB map data format | |
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Header (meta data) | emd-6445-v30.xml emd-6445.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | emd_6445.jpg | 45.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6445 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6445 | HTTPS FTP |
-Validation report
Summary document | emd_6445_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_6445_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_6445_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6445 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6445 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6445.map.gz / Format: CCP4 / Size: 500 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The whole map of BTV virion at pH 3.4 without imposing a reverse B-factor to boost high frequency signals | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.89 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 : BTV virion at pH 3.4 without imposing a reverse B-factor to boost...
Entire | Name: BTV virion at pH 3.4 without imposing a reverse B-factor to boost high frequency signals |
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Components |
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-Supramolecule #1000: BTV virion at pH 3.4 without imposing a reverse B-factor to boost...
Supramolecule | Name: BTV virion at pH 3.4 without imposing a reverse B-factor to boost high frequency signals type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Bluetongue virus 1
Supramolecule | Name: Bluetongue virus 1 / type: virus / ID: 1 / NCBI-ID: 35327 / Sci species name: Bluetongue virus 1 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Capra hircus (goat) / synonym: VERTEBRATES |
Virus shell | Shell ID: 1 / Diameter: 800 Å / T number (triangulation number): 13 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 3.4 / Details: citrate buffer |
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Grid | Details: thin carbon on a lacey holey carbon support film |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | May 11, 2011 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 350 / Bits/pixel: 32 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: OTHER / Software - Name: Frealign / Number images used: 4503 |