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- EMDB-20474: Poliovirus Type-1 Mahoney receptor catalysed 135S particle incuba... -

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Basic information

Entry
Database: EMDB / ID: EMD-20474
TitlePoliovirus Type-1 Mahoney receptor catalysed 135S particle incubated with anti-VP1 mAb for 1 hour at 37 degrees C
Map dataPoliovirus Type-1 Mahoney receptor catalysed 135S particle incubated with anti-VP1 mAb for 1 hr at 37% u02DAC.
Sample
  • Virus: Poliovirus type 1 (strain Mahoney)
Biological speciesPoliovirus type 1 (strain Mahoney)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHogle JM / Filman DJ / Shah PNM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI020566 United States
CitationJournal: PLoS Pathog / Year: 2020
Title: Cryo-EM structures reveal two distinct conformational states in a picornavirus cell entry intermediate.
Authors: Pranav N M Shah / David J Filman / Krishanthi S Karunatilaka / Emma L Hesketh / Elisabetta Groppelli / Mike Strauss / James M Hogle /
Abstract: The virions of enteroviruses such as poliovirus undergo a global conformational change after binding to the cellular receptor, characterized by a 4% expansion, and by the opening of holes at the two ...The virions of enteroviruses such as poliovirus undergo a global conformational change after binding to the cellular receptor, characterized by a 4% expansion, and by the opening of holes at the two and quasi-three-fold symmetry axes of the capsid. The resultant particle is called a 135S particle or A-particle and is thought to be on the pathway to a productive infection. Previously published studies have concluded that the membrane-interactive peptides, namely VP4 and the N-terminus of VP1, are irreversibly externalized in the 135S particle. However, using established protocols to produce the 135S particle, and single particle cryo-electron microscopy methods, we have identified at least two unique states that we call the early and late 135S particle. Surprisingly, only in the "late" 135S particles have detectable levels of the VP1 N-terminus been trapped outside the capsid. Moreover, we observe a distinct density inside the capsid that can be accounted for by VP4 that remains associated with the genome. Taken together our results conclusively demonstrate that the 135S particle is not a unique conformation, but rather a family of conformations that could exist simultaneously.
History
DepositionJul 16, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseAug 12, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 50
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 50
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20474.png

Downloads & links

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Map

FileDownload / File: emd_20474.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPoliovirus Type-1 Mahoney receptor catalysed 135S particle incubated with anti-VP1 mAb for 1 hr at 37% u02DAC.
Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy EMDB: 50 / Movie #1: 50
Minimum - Maximum0 - 100
Average (Standard dev.)23.861189 (±7.9438066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-224-224-224
Dimensions448448448
Spacing448448448
CellA=B=C: 497.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z497.280497.280497.280
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS-224-224-224
NC/NR/NS448448448
D min/max/mean0.000100.00023.861

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Supplemental data

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Sample components

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Entire : Poliovirus type 1 (strain Mahoney)

EntireName: Poliovirus type 1 (strain Mahoney)
Components
  • Virus: Poliovirus type 1 (strain Mahoney)

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Supramolecule #1: Poliovirus type 1 (strain Mahoney)

SupramoleculeName: Poliovirus type 1 (strain Mahoney) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 12081 / Sci species name: Poliovirus type 1 (strain Mahoney) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.0 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 300.0 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris-HCl, pH 7.5 + 2 mM CaCl2
GridSupport film - Material: CARBON / Support film - topology: LACEY / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 1.06 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1hxs

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 6682
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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