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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12595 | |||||||||
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Title | Rhinovirus-14 ICAM-1 empty particle at pH 6.2 | |||||||||
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![]() | rhinovirus 14 / RV14 / HRV14 / acidification / pH 6.2 / genome release / emptu / ICAM-1 / VIRUS | |||||||||
Function / homology | ![]() lysis of host organelle involved in viral entry into host cell / 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 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 ...lysis of host organelle involved in viral entry into host cell / 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 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 / protein complex oligomerization / monoatomic ion channel activity / 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Hrebik D / Plevka P | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 403.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.2 KB 22.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.1 KB | Display | ![]() |
Images | ![]() | 354.7 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() | 409.5 MB 409 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7numMC ![]() 7bg6C ![]() 7bg7C ![]() 7nulC ![]() 7nunC ![]() 7nuoC ![]() 7nuqC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.063 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #1
File | emd_12595_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_12595_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Rhinovirus B14
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Rhinovirus B14
Supramolecule | Name: Rhinovirus B14 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12131 / Sci species name: Rhinovirus B14 / Sci species strain: 1059 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7 MDa |
Virus shell | Shell ID: 1 / Name: Rhinovirus B14 / Diameter: 295.0 Å / T number (triangulation number): 3 |
-Macromolecule #1: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 32.975004 KDa |
Sequence | String: ALTEGLGDEL EEVIVEKTKQ TVASISSGPK HTQKVPILTA NETGATMPVL PSDSIETRTT YMHFNGSETD VECFLGRAAC VHVTEIQNK DATGIDNHRE AKLFNDWKIN LSSLVQLRKK LELFTYVRFD SEYTILATAS QPDSANYSSN LVVQAMYVPP G APNPKEWD ...String: ALTEGLGDEL EEVIVEKTKQ TVASISSGPK HTQKVPILTA NETGATMPVL PSDSIETRTT YMHFNGSETD VECFLGRAAC VHVTEIQNK DATGIDNHRE AKLFNDWKIN LSSLVQLRKK LELFTYVRFD SEYTILATAS QPDSANYSSN LVVQAMYVPP G APNPKEWD DYTWQSASNP SVFFKVGDTS RFSVPYVGLA SAYNCFYDGY SHDDAETQYG ITVLNHMGSM AFRIVNEHDE HK TLVKIRV YHRAKHVEAW IPRAPRALPY TSIGRTNYPK NTEPVIKKRK GDIKSY UniProtKB: Genome polyprotein |
-Macromolecule #2: P1
Macromolecule | Name: P1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.822299 KDa |
Sequence | String: 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 SQTV UniProtKB: Genome polyprotein |
-Macromolecule #3: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 28.501361 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL | |||||||||||||||
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Buffer | pH: 6.2 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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: 6548 / Average exposure time: 1.0 sec. / Average electron dose: 77.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.95 µm / Calibrated defocus min: 0.25 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |