[English] 日本語
Yorodumi
- EMDB-6445: Atomic structure of a non-enveloped virus reveals pH sensors for ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 6445
TitleAtomic structure of a non-enveloped virus reveals pH sensors for a coordinated process of cell entry
Map dataThe whole map of BTV virion at pH 3.4 without imposing a reverse B-factor to boost high frequency signals
SampleBTV virion at pH 3.4 without imposing a reverse B-factor to boost high frequency signals
  • virus
KeywordsNon-enveloped virus / cell entry / cryo-EM / pH sensor
SourceBluetongue virus 1 / virus
Methodsingle particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsZhang X / Patel A / Celma C / Roy P / Zhou ZH
CitationJournal: 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.
DateDeposition: Aug 27, 2015 / Header (metadata) release: Sep 23, 2015 / Map release: Dec 9, 2015 / Last update: Jan 20, 2016

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_6445.map.gz (map file in CCP4 format, 524289 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.89 Å/pix.
= 967.68 Å
512 pix
1.89 Å/pix.
= 967.68 Å
512 pix
1.89 Å/pix.
= 967.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.89 Å
Density
Contour Level:0.021 (by emdb), 0.01 (movie #1):
Minimum - Maximum-0.03486086 - 0.07199354
Average (Standard dev.)-0.00617108 (0.02015702)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin000
Limit511511511
Spacing512512512
CellA=B=C: 967.68 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.891.891.89
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z967.680967.680967.680
α/β/γ90.00090.00090.000
start NX/NY/NZ-8211244
NX/NY/NZ115138149
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0350.072-0.006

-
Supplemental data

-
Sample components

-
Entire BTV virion at pH 3.4 without imposing a reverse B-factor to boost...

EntireName: BTV virion at pH 3.4 without imposing a reverse B-factor to boost high frequency signals
Number of components: 1

-
Component #1: virus, Bluetongue virus 1

VirusName: Bluetongue virus 1Bluetongue disease / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Bluetongue virus 1 / virus
Source (natural)Host Species: Capra hircus / Goat / mammal / image: Capra aegagrus
Host category: VERTEBRATES

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: citrate buffer / pH: 3.4
Support filmthin carbon on a lacey holey carbon support film
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: May 11, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 350 / Sampling size: 15 microns / Bit depth: 32

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 4503
3D reconstructionAlgorithm: reference match / Software: Frealign / CTF correction: each particle / Resolution: 3.3 Å / Resolution method: FSC 0.143, semi-independent

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more