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- EMDB-20275: Poliovirus 135S-like expanded particle in complex with a monoclon... -

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Basic information

Entry
Database: EMDB / ID: EMD-20275
TitlePoliovirus 135S-like expanded particle in complex with a monoclonal antibody directed against the N-terminal extension of capsid protein VP1
Map dataSharpened Poliovirus 135S-like expanded particle in complex with a monoclonal antibody directed against the N-terminal extension of capsid protein VP1
SampleHuman poliovirus 1 Mahoney != Poliovirus type 1 (strain Mahoney)

Human poliovirus 1 Mahoney

  • Virus: Poliovirus type 1 (strain Mahoney)
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
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 RIG-I activity / 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 MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / 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 RIG-I activity / 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 MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont-mediated suppression of host innate immune response / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / 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) / Peptidase C3A/C3B, picornaviral ...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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesPoliovirus type 1 (strain Mahoney)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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 Diseases (NIH/NIAID)AI020566 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
DepositionJun 10, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseJun 10, 2020-
UpdateOct 21, 2020-
Current statusOct 21, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
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  • Surface view with fitted model
  • Atomic models: PDB-6p9o
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6p9o
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20275.png

Downloads & links

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Map

FileDownload / File: emd_20275.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Poliovirus 135S-like expanded particle in complex with a monoclonal antibody directed against the N-terminal extension of capsid protein VP1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 450 pix.
= 475.2 Å		1.06 Å/pix.
x 450 pix.
= 475.2 Å		1.06 Å/pix.
x 450 pix.
= 475.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.056 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.08444863 - 0.14032093
Average (Standard dev.)0.00016699648 (±0.008932629)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-225-225-225
Dimensions450450450
Spacing450450450
CellA=B=C: 475.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0561.0561.056
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z475.200475.200475.200
α/β/γ90.00090.00090.000
start NX/NY/NZ9482110
NX/NY/NZ11313776
MAP C/R/S123
start NC/NR/NS-225-225-225
NC/NR/NS450450450
D min/max/mean-0.0840.1400.000

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Supplemental data

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Mask #1

Fileemd_20275_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human poliovirus 1 Mahoney

EntireName: Human poliovirus 1 Mahoney
Components
  • Virus: Poliovirus type 1 (strain Mahoney)
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3

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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: all / 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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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus type 1 (strain Mahoney) / Strain: Mahoney
Molecular weightTheoretical: 33.488613 KDa
SequenceString: GLGQMLESMI DNTVRETVGA ATSRDALPNT EASGPTHSKE IPALTAVETG ATNPLVPSDT VQTRHVVQHR SRSESSIESF FARGACVTI MTVDNPASTT NKDKLFAVWK ITYKDTVQLR RKLEFFTYSR FDMELTFVVT ANFTETNNGH ALNQVYQIMY V PPGAPVPE ...String:
GLGQMLESMI DNTVRETVGA ATSRDALPNT EASGPTHSKE IPALTAVETG ATNPLVPSDT VQTRHVVQHR SRSESSIESF FARGACVTI MTVDNPASTT NKDKLFAVWK ITYKDTVQLR RKLEFFTYSR FDMELTFVVT ANFTETNNGH ALNQVYQIMY V PPGAPVPE KWDDYTWQTS SNPSIFYTYG TAPARISVPY VGISNAYSHF YDGFSKVPLK DQSAALGDSL YGAASLNDFG IL AVRVVND HNPTKVTSKI RVYLKPKHIR VWCPRPPRAV AYYGPGVDYK DGTLTPLSTK DLTTY

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus type 1 (strain Mahoney) / Strain: Mahoney
Molecular weightTheoretical: 30.075783 KDa
SequenceString: SPNIEACGYS DRVLQLTLGN STITTQEAAN SVVAYGRWPE YLRDSEANPV DQPTEPDVAA CRFYTLDTVS WTKESRGWWW KLPDALRDM GLFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAVPE MCLAGDSNTT TMHTSYQNAN PGEKGGTFTG T FTPDNNQT ...String:
SPNIEACGYS DRVLQLTLGN STITTQEAAN SVVAYGRWPE YLRDSEANPV DQPTEPDVAA CRFYTLDTVS WTKESRGWWW KLPDALRDM GLFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAVPE MCLAGDSNTT TMHTSYQNAN PGEKGGTFTG T FTPDNNQT SPARRFCPVD YLLGNGTLLG NAFVFPHQII NLRTNNCATL VLPYVNSLSI DSMVKHNNWG IAILPLAPLN FA SESSPEI PITLTIAPMC CEFNGLRNIT LPRLQ

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus type 1 (strain Mahoney) / Strain: Mahoney
Molecular weightTheoretical: 26.547482 KDa
SequenceString: GLPVMNTPGS NQYLTADNFQ SPCALPEFDV TPPIDIPGEV KNMMELAEID TMIPFDLSAT KKNTMEMYRV RLSDKPHTDD PILCLSLSP ASDPRLSHTM LGEILNYYTH WAGSLKFTFL FCGSMMATGK LLVSYAPPGA DPPKKRKEAM LGTHVIWDIG L QSSCTMVV ...String:
GLPVMNTPGS NQYLTADNFQ SPCALPEFDV TPPIDIPGEV KNMMELAEID TMIPFDLSAT KKNTMEMYRV RLSDKPHTDD PILCLSLSP ASDPRLSHTM LGEILNYYTH WAGSLKFTFL FCGSMMATGK LLVSYAPPGA DPPKKRKEAM LGTHVIWDIG L QSSCTMVV PWISNTTYRQ TIDDSFTEGG YISVFYQTRI VVPLSTPREM DILGFVSACN DFSVRLLRDT THIEQKALAQ

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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: phosphate-buffered saline
GridMaterial: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Average electron dose: 2.17 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / 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

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 20062
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6p9o:
Poliovirus 135S-like expanded particle in complex with a monoclonal antibody directed against the N-terminal extension of capsid protein VP1

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