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- EMDB-5291: Poliovirus 160S particle and C3 Fab complex at 11.1 Angstrom reso... -

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Basic information

Entry
Database: EMDB / ID: EMD-5291
TitlePoliovirus 160S particle and C3 Fab complex at 11.1 Angstrom resolution
Map dataThis is a map of poliovirus 160S particle and C3 Fab complex.
Sample
  • Sample: Poliovirus 160S particle and C3 Fab complex
  • Virus: Human poliovirus 1 Mahoney
  • Protein or peptide: C3 Fab
Keywordspoliovirus / antibody-antigen interactions / antibody-protein interactions / C3 antibody / fragment antibody-binding (Fab) / picornavirus / virus-antibody interactions
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse) / Human poliovirus 1 Mahoney
Methodsingle particle reconstruction / cryo EM / Resolution: 11.1 Å
AuthorsLin J / Cheng N / Hogle JM / Steven AC / Belnap DM
CitationJournal: J Immunol / Year: 2013
Title: Conformational shift of a major poliovirus antigen confirmed by immuno-cryogenic electron microscopy.
Authors: Jun Lin / Naiqian Cheng / James M Hogle / Alasdair C Steven / David M Belnap /
Abstract: Small, interfacial conformational changes occur in some Ag-Ab interactions. Using cryogenic electron microscopy (cryo-EM), we have demonstrated such changes in a major antigenic site of a poliovirus ...Small, interfacial conformational changes occur in some Ag-Ab interactions. Using cryogenic electron microscopy (cryo-EM), we have demonstrated such changes in a major antigenic site of a poliovirus capsid protein. During cell entry, native human poliovirus (160S particle) converts to a cell entry intermediate (135S particle) and later to an RNA-released (80S) particle. By mixing particles with Fabs of the neutralizing C3 mAb, we labeled the external loop connecting the B and C β-strands (BC loop) of the capsid protein VP1 (residues 95-105) in the 160S and 135S states. We then determined three-dimensional structures by cryo-EM and enhanced their interpretability by fitting high-resolution coordinates of C3 Fab and the capsid proteins into the density maps. Binding of C3 to either 160S or 135S particles caused residues of the BC loop, located on the tip of a prominent peak known as the "mesa," to move by an estimated 5 Å. C3 Abs are neutralizing and can bind bivalently. The orientation of the bound Fabs in our reconstructions suggests that C3 neutralizes poliovirus by binding two adjacent BC loops on the same mesa and inhibiting conformational changes in the viral capsid.
History
DepositionMay 18, 2011-
Header (metadata) releaseOct 26, 2011-
Map releaseMay 31, 2012-
UpdateAug 14, 2013-
Current statusAug 14, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 45.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 45.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j3o
  • Surface level: 45.6
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j3o
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5291_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5291.map.gz / Format: CCP4 / Size: 56.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of poliovirus 160S particle and C3 Fab complex.
Voxel sizeX=Y=Z: 1.824 Å
Density
Contour LevelBy AUTHOR: 45.600000000000001 / Movie #1: 45.6
Minimum - Maximum-82.283203130000004 - 276.944366460000026
Average (Standard dev.)19.680618290000002 (±51.859786990000003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-123-123-123
Dimensions247247247
Spacing248248248
CellA=B=C: 452.352 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.8241.8241.824
M x/y/z248248248
origin x/y/z0.0000.0000.000
length x/y/z452.352452.352452.352
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-123-123-123
NC/NR/NS247247247
D min/max/mean-82.283276.94419.681

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Supplemental data

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Sample components

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Entire : Poliovirus 160S particle and C3 Fab complex

EntireName: Poliovirus 160S particle and C3 Fab complex
Components
  • Sample: Poliovirus 160S particle and C3 Fab complex
  • Virus: Human poliovirus 1 Mahoney
  • Protein or peptide: C3 Fab

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Supramolecule #1000: Poliovirus 160S particle and C3 Fab complex

SupramoleculeName: Poliovirus 160S particle and C3 Fab complex / type: sample / ID: 1000 / Oligomeric state: 160S particle icosahedral with Fab / Number unique components: 2

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Supramolecule #1: Human poliovirus 1 Mahoney

SupramoleculeName: Human poliovirus 1 Mahoney / type: virus / ID: 1 / NCBI-ID: 12081 / Sci species name: Human poliovirus 1 Mahoney / Sci species strain: Mahoney / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 325 Å / T number (triangulation number): 1

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Macromolecule #1: C3 Fab

MacromoleculeName: C3 Fab / type: protein_or_peptide / ID: 1 / Name.synonym: C3 Fab / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Mus musculus (house mouse)

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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

BufferpH: 7.5 / Details: 20 mM Tris, 2 mM CaCl2
VitrificationCryogen name: ETHANE / Instrument: OTHER
Details: Vitrification carried out in ambient atmosphere. Ethane cooled by liquid nitrogen.
Method: Blotted manually before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 37587 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 1.77 µm / Nominal defocus min: 0.73 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedureLegacy - Astigmatism: Bsoft
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 12 / Average electron dose: 10 e/Å2 / Details: Defocal pairs were used. / Bits/pixel: 8
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: CTF and decay correction of each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EM3DR2
Details: Reconstruction computed from focal pairs. Pairs not summed for reconstruction calculation.
Number images used: 4184

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Atomic model buiding 1

Initial modelPDB ID:

1fpt


Chain - #0 - Chain ID: L / Chain - #1 - Chain ID: H / Chain - #2 - Chain ID: P
SoftwareName: CHARMM
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body. Atomic coordinates for the C3 Fab (Nature Struct. Biol. 2, 232-243) (1FPT in Protein Data Bank) were first fitted manually (by eye) via UCSF Chimera package (Journal of Computational Chemistry 25, 1605-1612). Next, a core-weighted, rigid-body fitting algorithm, implemented in CHARRM (J Struct Biol 141, 63-76), was used to refine the fit.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3j3o:
Conformational Shift of a Major Poliovirus Antigen Confirmed by Immuno-Cryogenic Electron Microscopy: 160S Poliovirus and C3-Fab Complex

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