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- EMDB-5292: Poliovirus 135S particle and C3 Fab complex at 9.1 Angstrom resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-5292
TitlePoliovirus 135S particle and C3 Fab complex at 9.1 Angstrom resolution
Map dataThis is a map of poliovirus 135S particle and C3 Fab complex.
Sample
  • Sample: Poliovirus 135S particle and C3 Fab complex
  • Virus: Human poliovirus 1 Mahoney
Keywords135S cell-entry intermediate particle / 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 / positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding ...symbiont-mediated suppression of host translation initiation / positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / endosome to lysosome transport / positive regulation of endocytosis / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / immunoglobulin mediated immune response / antigen processing and presentation / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / multivesicular body / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / response to bacterium / endocytosis involved in viral entry into host cell / : / positive regulation of immune response / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / antibacterial humoral response / 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 / virion attachment to host cell / structural molecule activity / proteolysis / extracellular space / RNA binding / ATP binding / membrane / metal ion binding / plasma membrane / cytosol
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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ig gamma-2A chain C region, membrane-bound form / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1 Mahoney
Methodsingle particle reconstruction / cryo EM / Resolution: 9.1 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 19, 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: 27.1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 27.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j3p
  • Surface level: 27.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j3p
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5292_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5292.map.gz / Format: CCP4 / Size: 70.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of poliovirus 135S particle and C3 Fab complex.
Voxel sizeX=Y=Z: 1.84 Å
Density
Contour LevelBy AUTHOR: 27.100000000000001 / Movie #1: 27.1
Minimum - Maximum-41.275337219999997 - 163.060073850000009
Average (Standard dev.)11.427649499999999 (±31.435911180000002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-133-133-133
Dimensions267267267
Spacing267267267
CellA=B=C: 491.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.841.841.84
M x/y/z267267267
origin x/y/z0.0000.0000.000
length x/y/z491.280491.280491.280
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-133-133-133
NC/NR/NS267267267
D min/max/mean-41.275163.06011.428

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Supplemental data

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Sample components

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Entire : Poliovirus 135S particle and C3 Fab complex

EntireName: Poliovirus 135S particle and C3 Fab complex
Components
  • Sample: Poliovirus 135S particle and C3 Fab complex
  • Virus: Human poliovirus 1 Mahoney

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Supramolecule #1000: Poliovirus 135S particle and C3 Fab complex

SupramoleculeName: Poliovirus 135S particle and C3 Fab complex / type: sample / ID: 1000 / Oligomeric state: 135S 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
Details: native virus 160S is converted by heat treatment to 135S
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: 340 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

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: 38000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 1.63 µm / Nominal defocus min: 1.12 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: 4 / 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: 9.1 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: 9810

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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-3j3p:
Conformational Shift of a Major Poliovirus Antigen Confirmed by Immuno-Cryogenic Electron Microscopy: 135S Poliovirus and C3-Fab Complex

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