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- EMDB-8284: expanded poliovirus in complex with VHH 12B -

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Basic information

Entry
Database: EMDB / ID: EMD-8284
Titleexpanded poliovirus in complex with VHH 12B
Map data
Sampleexpanded poliovirus in complex with VHH 12B:
VP1 / VP2 / Genome polyprotein / VHH 12B
Function / homology
Function and homology information


suppression by virus of host translation initiation factor activity / suppression by virus of host MDA-5 activity / suppression by virus of host RIG-I activity / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / picornain 3C / suppression by virus of host MAVS activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...suppression by virus of host translation initiation factor activity / suppression by virus of host MDA-5 activity / suppression by virus of host RIG-I activity / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / picornain 3C / suppression by virus of host MAVS activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / RNA-protein covalent cross-linking / positive stranded viral RNA replication / integral to membrane of host cell / pore formation by virus in membrane of host cell / viral capsid / virion assembly / endocytosis involved in viral entry into host cell / protein complex oligomerization / nucleoside-triphosphate phosphatase / ion channel activity / induction by virus of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA helicase activity / transcription, DNA-templated / virion attachment to host cell / host cell nucleus / structural molecule activity / RNA binding / membrane / ATP binding / metal ion binding
Viral coat protein subunit / Picornavirus coat protein VP4 / Poliovirus core protein 3a, soluble domain / Peptidase C3, picornavirus core protein 2A / Picornavirus/Calicivirus coat protein / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / Reverse transcriptase/Diguanylate cyclase domain ...Viral coat protein subunit / Picornavirus coat protein VP4 / Poliovirus core protein 3a, soluble domain / Peptidase C3, picornavirus core protein 2A / Picornavirus/Calicivirus coat protein / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / Reverse transcriptase/Diguanylate cyclase domain / Picornavirus 2B protein / DNA/RNA polymerase superfamily / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Helicase, superfamily 3, single-stranded RNA virus / Poliovirus 3A protein-like / Picornavirales 3C/3C-like protease domain / P-loop containing nucleoside triphosphate hydrolase
Genome polyprotein
Biological speciesPoliovirus type 1 (strain Mahoney) / Poliovirus type 1 / Camelus dromedarius (Arabian camel)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsStrauss M / Schotte L / Filman DJ / Hogle JM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI020566 United States
CitationJournal: J Virol / Year: 2017
Title: Cryo-electron Microscopy Structures of Expanded Poliovirus with VHHs Sample the Conformational Repertoire of the Expanded State.
Authors: Mike Strauss / Lise Schotte / Krishanthi S Karunatilaka / David J Filman / James M Hogle /
Abstract: By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs ...By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs bind to a site on the top surface of the capsid protein VP3, which is hidden in the native virus. Interestingly, although the four VHHs bind to the same site, the structures of the expanded virus differ in detail in each complex, suggesting that each of the Nanobodies has sampled a range of low-energy structures available to the expanded virion. By stabilizing unique structures of expanded virions, VHH binding permitted a more detailed view of the virus structure than was previously possible, leading to a better understanding of the expansion process that is a critical step in infection. It is now clear which polypeptide chains become disordered and which become rearranged. The higher resolution of these structures also revealed well-ordered conformations for the EF loop of VP2, the GH loop of VP3, and the N-terminal extensions of VP1 and VP2, which, in retrospect, were present in lower-resolution structures but not recognized. These structural observations help to explain preexisting mutational data and provide insights into several other stages of the poliovirus life cycle, including the mechanism of receptor-triggered virus expansion.
Importance: When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The ...Importance: When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The structures of poliovirus bound to single-domain antibodies presented here capture the altered virus in what appear to be intermediate states. A careful analysis of these structures lets us better understand the molecular mechanism of infection and how these changes in the virus lead to productive-infection events.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 25, 2016-
Header (metadata) releaseSep 28, 2016-
Map releaseNov 2, 2016-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0065
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0065
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5ktz
  • Surface level: 0.0065
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5ktz
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8284.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 512 pix.
= 504.832 Å
0.99 Å/pix.
x 512 pix.
= 504.832 Å
0.99 Å/pix.
x 512 pix.
= 504.832 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.986 Å
Density
Contour LevelBy EMDB: 0.009 / Movie #1: 0.0065
Minimum - Maximum-0.0045212684 - 0.019152572
Average (Standard dev.)-0.0009854144 (±0.003261853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 504.832 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9860.9860.986
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z504.832504.832504.832
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-0.0050.019-0.001

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Supplemental data

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Sample components

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Entire expanded poliovirus in complex with VHH 12B

EntireName: expanded poliovirus in complex with VHH 12B / Number of components: 5

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Component #1: protein, expanded poliovirus in complex with VHH 12B

ProteinName: expanded poliovirus in complex with VHH 12B / Recombinant expression: No
MassTheoretical: 9 MDa
SourceSpecies: Poliovirus type 1 (strain Mahoney)

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Component #2: protein, VP1

ProteinName: VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.291594 kDa
SourceSpecies: Poliovirus type 1 (strain Mahoney) / Strain: Mahoney
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, VP2

ProteinName: VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.677301 kDa
SourceSpecies: Poliovirus type 1 (strain Mahoney) / Strain: Mahoney
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Genome polyprotein

ProteinName: Genome polyprotein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.777613 kDa
SourceSpecies: Poliovirus type 1 / Strain: Mahoney
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, VHH 12B

ProteinName: VHH 12B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.072334 kDa
SourceSpecies: Camelus dromedarius (Arabian camel)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.45 mg/mL / pH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 17627
3D reconstructionSoftware: GeFrealign, FREALIGN / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: RECIPROCAL
Details: Fitting protocol: rigid body restraint of structurally conserved areas, and stereochemically restrained, icosahedrally restrained flexible fitting of areas that would otherwise disagree with ...Details: Fitting protocol: rigid body restraint of structurally conserved areas, and stereochemically restrained, icosahedrally restrained flexible fitting of areas that would otherwise disagree with the map. Refinement space: reciprocal, using both Fourier amplitudes and phases.
Output model

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