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.
Electron dose: 20 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Image scans
Num. digital images: 1630
-
Processing
EM software
Name: FREALIGN / Category: 3D reconstruction
CTF correction
Details: each particle
Symmetry
Point symmetry: I (icosahedral)
3D reconstruction
Method: reference match / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5008 / Nominal pixel size: 1.01 Å / Actual pixel size: 1.01 Å / Symmetry type: POINT
Refinement
Resolution: 3.3→3.3 Å / SU ML: 0.38 / σ(F): 2 / Phase error: 22.14 / Stereochemistry target values: MLHL
Rfactor
Num. reflection
% reflection
Rfree
0.1808
456
0.06 %
Rwork
0.1826
784934
-
obs
0.1826
785390
99.95 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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