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- EMDB-12171: HRV14 native particle -

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Basic information

Entry
Database: EMDB / ID: EMD-12171
TitleHRV14 native particle
Map dataB-factor sharpened map (-42) of native particle of HRV14
Sample
  • Virus: Rhinovirus B14
    • RNA: RNA-octamer (5'-R(P*UP*GP*UP*UP*UP*UP*UP*A)-3')
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
  • Ligand: water
Keywordsenterovirus / rhinovirus 14 / HRV14 / RV14 / native particle / VIRUS
Function / homology
Function and homology information


lysis of host organelle involved in viral entry into host cell / protein complex oligomerization / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / monoatomic ion channel 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 / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...lysis of host organelle involved in viral entry into host cell / protein complex oligomerization / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / monoatomic ion channel 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 / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / DNA replication / RNA helicase activity / 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 / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / 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) ...Picornavirus coat protein VP4 superfamily / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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
Biological speciesRhinovirus B14 / Human rhinovirus 14
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsHrebik D / Fuzik T
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Czech Science Foundation19-25982X Czech Republic
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating.
Authors: Dominik Hrebík / Tibor Füzik / Mária Gondová / Lenka Šmerdová / Athanassios Adamopoulos / Ondrej Šedo / Zbyněk Zdráhal / Pavel Plevka /
Abstract: Most rhinoviruses, which are the leading cause of the common cold, utilize intercellular adhesion molecule-1 (ICAM-1) as a receptor to infect cells. To release their genomes, rhinoviruses convert to ...Most rhinoviruses, which are the leading cause of the common cold, utilize intercellular adhesion molecule-1 (ICAM-1) as a receptor to infect cells. To release their genomes, rhinoviruses convert to activated particles that contain pores in the capsid, lack minor capsid protein VP4, and have an altered genome organization. The binding of rhinoviruses to ICAM-1 promotes virus activation; however, the molecular details of the process remain unknown. Here, we present the structures of virion of rhinovirus 14 and its complex with ICAM-1 determined to resolutions of 2.6 and 2.4 Å, respectively. The cryo-electron microscopy reconstruction of rhinovirus 14 virions contains the resolved density of octanucleotide segments from the RNA genome that interact with VP2 subunits. We show that the binding of ICAM-1 to rhinovirus 14 is required to prime the virus for activation and genome release at acidic pH. Formation of the rhinovirus 14-ICAM-1 complex induces conformational changes to the rhinovirus 14 capsid, including translocation of the C termini of VP4 subunits, which become poised for release through pores that open in the capsids of activated particles. VP4 subunits with altered conformation block the RNA-VP2 interactions and expose patches of positively charged residues. The conformational changes to the capsid induce the redistribution of the virus genome by altering the capsid-RNA interactions. The restructuring of the rhinovirus 14 capsid and genome prepares the virions for conversion to activated particles. The high-resolution structure of rhinovirus 14 in complex with ICAM-1 explains how the binding of uncoating receptors enables enterovirus genome release.
History
DepositionJan 6, 2021-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bg6
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bg6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12171.png

Downloads & links

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Map

FileDownload / File: emd_12171.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened map (-42) of native particle of HRV14
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 380 pix.
= 403.94 Å		1.06 Å/pix.
x 380 pix.
= 403.94 Å		1.06 Å/pix.
x 380 pix.
= 403.94 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-9.077759 - 13.779369000000001
Average (Standard dev.)0.000000004582036 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-190-190-190
Dimensions380380380
Spacing380380380
CellA=B=C: 403.93997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z403.940403.940403.940
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-190-190-190
NC/NR/NS380380380
D min/max/mean-9.07813.7790.000

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Supplemental data

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Mask #1

Fileemd_12171_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Locally sharpened map by LocalDeblur of native particle of HRV14

Fileemd_12171_additional_1.map
AnnotationLocally sharpened map by LocalDeblur of native particle of HRV14
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of native particle of HRV14 at...

Fileemd_12171_additional_2.map
AnnotationUnsharpened map of native particle of HRV14 at a resolution of 3.6 A with visible patches of RNA octamers.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Mask used for calculation of the FSC curve in relion postprocess.

Fileemd_12171_additional_3.map
AnnotationMask used for calculation of the FSC curve in relion postprocess.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ewald sphere corrected half map 1 used in relion postprocess

Fileemd_12171_half_map_1.map
AnnotationEwald sphere corrected half map 1 used in relion postprocess
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ewald sphere corrected half map 2 used in relion postprocess

Fileemd_12171_half_map_2.map
AnnotationEwald sphere corrected half map 2 used in relion postprocess
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rhinovirus B14

EntireName: Rhinovirus B14
Components
  • Virus: Rhinovirus B14
    • RNA: RNA-octamer (5'-R(P*UP*GP*UP*UP*UP*UP*UP*A)-3')
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
  • Ligand: water

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Supramolecule #1: Rhinovirus B14

SupramoleculeName: Rhinovirus B14 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / NCBI-ID: 12131 / Sci species name: Rhinovirus B14 / Sci species strain: 1059 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Molecular weightTheoretical: 8.5 MDa
Virus shellShell ID: 1 / Name: rhinovirus 14 / Diameter: 310.0 Å / T number (triangulation number): 3

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Macromolecule #1: RNA-octamer (5'-R(P*UP*GP*UP*UP*UP*UP*UP*A)-3')

MacromoleculeName: RNA-octamer (5'-R(P*UP*GP*UP*UP*UP*UP*UP*A)-3') / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Rhinovirus B14
Molecular weightTheoretical: 2.466449 KDa
SequenceString:
UGUUUUUA

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Macromolecule #2: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Human rhinovirus 14
Molecular weightTheoretical: 30.789572 KDa
SequenceString: TVASISSGPK HTQKVPILTA NETGATMPVL PSDSIETRTT YMHFNGSETD VECFLGRAAC VHVTEIQNKD ATGIDNHREA KLFNDWKIN LSSLVQLRKK LELFTYVRFD SEYTILATAS QPDSANYSSN LVVQAMYVPP GAPNPKEWDD YTWQSASNPS V FFKVGDTS ...String:
TVASISSGPK HTQKVPILTA NETGATMPVL PSDSIETRTT YMHFNGSETD VECFLGRAAC VHVTEIQNKD ATGIDNHREA KLFNDWKIN LSSLVQLRKK LELFTYVRFD SEYTILATAS QPDSANYSSN LVVQAMYVPP GAPNPKEWDD YTWQSASNPS V FFKVGDTS RFSVPYVGLA SAYNCFYDGY SHDDAETQYG ITVLNHMGSM AFRIVNEHDE HKTLVKIRVY HRAKHVEAWI PR APRALPY TSIGRTNYPK NTEPVIKKRK GDIKSY

UniProtKB: Genome polyprotein

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Macromolecule #3: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Human rhinovirus 14
Molecular weightTheoretical: 28.501361 KDa
SequenceString: SPNVEACGYS DRVQQITLGN STITTQEAAN AVVCYAEWPE YLPDVDASDV NKTSKPDTSV CRFYTLDSKT WTTGSKGWCW KLPDALKDM GVFGQNMFFH SLGRSGYTVH VQCNATKFHS GCLLVVVIPE HQLASHEGGN VSVKYTFTHP GERGIDLSSA N EVGGPVKD ...String:
SPNVEACGYS DRVQQITLGN STITTQEAAN AVVCYAEWPE YLPDVDASDV NKTSKPDTSV CRFYTLDSKT WTTGSKGWCW KLPDALKDM GVFGQNMFFH SLGRSGYTVH VQCNATKFHS GCLLVVVIPE HQLASHEGGN VSVKYTFTHP GERGIDLSSA N EVGGPVKD VIYNMNGTLL GNLLIFPHQF INLRTNNTAT IVIPYINSVP IDSMTRHNNV SLMVIPIAPL TVPTGATPSL PI TVTIAPM CTEFSGIRSK SIVPQ

UniProtKB: Genome polyprotein

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Macromolecule #4: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Human rhinovirus 14
Molecular weightTheoretical: 26.236754 KDa
SequenceString: GLPTTTLPGS GQFLTTDDRQ SPSALPNYEP TPRIHIPGKV HNLLEIIQVD TLIPMNNTHT KDEVNSYLIP LNANRQNEQV FGTNLFIGD GVFKTTLLGE IVQYYTHWSG SLRFSLMYTG PALSSAKLIL AYTPPGARGP QDRREAMLGT HVVWDIGLQS T IVMTIPWT ...String:
GLPTTTLPGS GQFLTTDDRQ SPSALPNYEP TPRIHIPGKV HNLLEIIQVD TLIPMNNTHT KDEVNSYLIP LNANRQNEQV FGTNLFIGD GVFKTTLLGE IVQYYTHWSG SLRFSLMYTG PALSSAKLIL AYTPPGARGP QDRREAMLGT HVVWDIGLQS T IVMTIPWT SGVQFRYTDP DTYTSAGFLS CWYQTSLILP PETTGQVYLL SFISACPDFK LRLMKDTQTI SQTVALTE

UniProtKB: Genome polyprotein

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Macromolecule #5: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Human rhinovirus 14
Molecular weightTheoretical: 7.183863 KDa
SequenceString:
GAQVSTQKSG SHENQNILTN GSNQTFTVIN YYKDAASTSS AGQSLSMDPS KFTEPVKDLM LKGAPALN

UniProtKB: Genome polyprotein

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 232 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
10.0 mMNa2HPO4disodium phosphate
1.8 mMKH2PO4monopotassium phosphate
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride

Details: PBS with ph = 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 6247 / Average exposure time: 1.0 sec. / Average electron dose: 83.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.4 µm / Calibrated defocus min: 0.32 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000
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

Particle selectionNumber selected: 3844
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4rhv

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 3343
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 1000 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4rhv


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 8.42 / Target criteria: Correlation coefficient
Output model

PDB-7bg6:
HRV14 native particle solved by cryoEM

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