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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8189 | |||||||||
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Title | CryoEM structure of the full virion of a human rhinovirus C | |||||||||
![]() | CryoEM structure of the full virion of a human rhinovirus C | |||||||||
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![]() | virus / jelly roll | |||||||||
Function / homology | ![]() 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 / ribonucleoside triphosphate phosphatase activity / 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 ...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 / ribonucleoside triphosphate phosphatase activity / 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 / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.79 Å | |||||||||
![]() | Liu Y / Hill MG | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Atomic structure of a rhinovirus C, a virus species linked to severe childhood asthma. Authors: Yue Liu / Marchel G Hill / Thomas Klose / Zhenguo Chen / Kelly Watters / Yury A Bochkov / Wen Jiang / Ann C Palmenberg / Michael G Rossmann / ![]() Abstract: Isolates of rhinovirus C (RV-C), a recently identified Enterovirus (EV) species, are the causative agents of severe respiratory infections among children and are linked to childhood asthma ...Isolates of rhinovirus C (RV-C), a recently identified Enterovirus (EV) species, are the causative agents of severe respiratory infections among children and are linked to childhood asthma exacerbations. The RV-C have been refractory to structure determination because they are difficult to propagate in vitro. Here, we report the cryo-EM atomic structures of the full virion and native empty particle (NEP) of RV-C15a. The virus has 60 "fingers" on the virus outer surface that probably function as dominant immunogens. Because the NEPs also display these fingers, they may have utility as vaccine candidates. A sequence-conserved surface depression adjacent to each finger forms a likely binding site for the sialic acid on its receptor. The RV-C, unlike other EVs, are resistant to capsid-binding antiviral compounds because the hydrophobic pocket in VP1 is filled with multiple bulky residues. These results define potential molecular determinants for designing antiviral therapeutics and vaccines. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 395.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.4 KB 20.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19.7 KB | Display | ![]() |
Images | ![]() | 258.6 KB | ||
Filedesc metadata | ![]() | 7.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 609.4 KB | Display | ![]() |
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Full document | ![]() | 609 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5k0uMC ![]() 8184C ![]() 5jzgC 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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Annotation | CryoEM structure of the full virion of a human rhinovirus C | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Rhinovirus C15a
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Rhinovirus C15a
Supramolecule | Name: Rhinovirus C15a / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: The cDNA of RV-C15 isolate was used to produce RNA transcripts in vitro, which were then used for transfection in HeLa WisL cells. The resultant recombinant RV-C15 virus was adapted in HeLa ...Details: The cDNA of RV-C15 isolate was used to produce RNA transcripts in vitro, which were then used for transfection in HeLa WisL cells. The resultant recombinant RV-C15 virus was adapted in HeLa cells expressing the RV-C receptor CDHR3 via multiple passage. The derivative was the RV-C15a virus. NCBI-ID: 463676 / Sci species name: Rhinovirus C15a / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() |
Molecular weight | Theoretical: 8.3 MDa |
Virus shell | Shell ID: 1 / Name: Capsid (p3) / Diameter: 300.0 Å / T number (triangulation number): 3 |
-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 31.802623 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: NNDDPVENFV ESTLKEVLVV PDTKPSGPQH TTKPSILGAM EIGASSNATP ESTIETRYVY NTNTNAEADV EMFLGRSALW GKVTLTRQY AKWEINFQEQ AHIRKKFEFF TYLRFDMEVT IVTNNKGLMQ IMFVPPGIDH PETHDDRKWD SASNPSVFFQ P KSGFPRFT ...String: NNDDPVENFV ESTLKEVLVV PDTKPSGPQH TTKPSILGAM EIGASSNATP ESTIETRYVY NTNTNAEADV EMFLGRSALW GKVTLTRQY AKWEINFQEQ AHIRKKFEFF TYLRFDMEVT IVTNNKGLMQ IMFVPPGIDH PETHDDRKWD SASNPSVFFQ P KSGFPRFT IPFTGLASAY YMFYDGYDKP KGSDNNEYGI APTNDMGLLC FRTLDNSGGN DVKIYVKPKH ITAWVPRPPR AT QYTHKYS TNYHYKPNSS GPDEHVLKDR HFIKTRPLIS SA UniProtKB: Genome polyprotein |
-Macromolecule #2: Capsid protein VP3
Macromolecule | Name: Capsid protein VP3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.965037 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GLPTRLPSGS QQFMTTEDEQ SPNILPGFHP SKKIHIPGMI TNVMHMARVD SFIPINNIQG EVGKVSMYYI TVTKKTVTER ILVLPLEMS NTLFATTLLG EVLNYYANWS GSITITFMCV CDAFSTGKFL VAYTPPGGKL PEDRKQAMLG VHIIWDLGLQ S SCTIVVPW ...String: GLPTRLPSGS QQFMTTEDEQ SPNILPGFHP SKKIHIPGMI TNVMHMARVD SFIPINNIQG EVGKVSMYYI TVTKKTVTER ILVLPLEMS NTLFATTLLG EVLNYYANWS GSITITFMCV CDAFSTGKFL VAYTPPGGKL PEDRKQAMLG VHIIWDLGLQ S SCTIVVPW ISSGFYRRTK ADSFTHGGYV SLWYQTAFVP PVSGGTGSIL ATCSACPDMS VRMLRDSPMM EQKNELQ UniProtKB: Genome polyprotein |
-Macromolecule #3: Capsid protein VP2
Macromolecule | Name: Capsid protein VP2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 29.090658 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: SPSVEACGYS DRLKQITIGN STITTQDSLH TVLAYGEWPT YLSDIDATSV DKPTHPETSA DRFYTLDSVE WQVGSHGWWW KLPDALKDM GVFGQNMYYH SMGRSGFIIH TQCNATKFHS GALIVAVIPE HQLAYVGGVK VNVGYDHTHP GQSGHQIRGP S QSNDRSGG ...String: SPSVEACGYS DRLKQITIGN STITTQDSLH TVLAYGEWPT YLSDIDATSV DKPTHPETSA DRFYTLDSVE WQVGSHGWWW KLPDALKDM GVFGQNMYYH SMGRSGFIIH TQCNATKFHS GALIVAVIPE HQLAYVGGVK VNVGYDHTHP GQSGHQIRGP S QSNDRSGG KPDEDPLFNC NGTLLGNITI FPHQIINLRT NNSSTIVVPY INCVPMDNML KHNNLSLVII PLVPLRPGSS GI NSVPITV TIAPYKSEFS GAMEAQRQ UniProtKB: Genome polyprotein |
-Macromolecule #4: Capsid protein VP4
Macromolecule | Name: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.174758 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GAQVSRQNNG THENGVTASN GSVIKYFNIN YYKDSASSGL SRQDFSQDPS KFTQPLVDTL TNPALM UniProtKB: Genome polyprotein |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 60 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Ultra thin Lacey carbon / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: LACEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 3-70 / Number grids imaged: 3 / Number real images: 8973 / Average exposure time: 14.0 sec. / Average electron dose: 25.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 0.7000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 14000 |
Sample stage | Specimen 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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |
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Output model | ![]() PDB-5k0u: |