+Open data
-Basic information
Entry | Database: PDB / ID: 7bg7 | ||||||
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Title | HRV14 in complex with its receptor ICAM-1 | ||||||
Components |
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Keywords | VIRUS / enterovirus / rhinovirus 14 / HRV14 / RV14 / native particle / receptor / virus-receptor complex / ICAM-1 | ||||||
Function / homology | Function and homology information regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / lysis of host organelle involved in viral entry into host cell / adhesion of symbiont to host / establishment of endothelial barrier ...regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / lysis of host organelle involved in viral entry into host cell / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / leukocyte migration / Interleukin-10 signaling / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / immunological synapse / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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 / cellular response to leukemia inhibitory factor / cellular response to glucose stimulus / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / cellular response to amyloid-beta / transmembrane signaling receptor activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / integrin binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / virus receptor activity / signaling receptor activity / symbiont-mediated suppression of host gene expression / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / DNA replication / RNA helicase activity / receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / cell adhesion / induction by virus of host autophagy / membrane raft / RNA-directed RNA polymerase / external side of plasma membrane / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / focal adhesion / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular space / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human rhinovirus 14 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||
Authors | Hrebik, D. / Fuzik, T. / Plevka, P. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7bg7.cif.gz | 181.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bg7.ent.gz | 143.5 KB | Display | PDB format |
PDBx/mmJSON format | 7bg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bg7_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7bg7_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7bg7_validation.xml.gz | 48.6 KB | Display | |
Data in CIF | 7bg7_validation.cif.gz | 72.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/7bg7 ftp://data.pdbj.org/pub/pdb/validation_reports/bg/7bg7 | HTTPS FTP |
-Related structure data
Related structure data | 12172MC 7bg6C 7nulC 7numC 7nunC 7nuoC 7nuqC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 5 molecules 1234B
#1: Protein | Mass: 32975.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 References: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
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#2: Protein | Mass: 28501.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 References: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#3: Protein | Mass: 26236.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 References: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#4: Protein | Mass: 7183.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 References: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#5: Protein | Mass: 49552.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ICAM1 / Plasmid: bacmid / Cell (production host): SF9 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P05362 |
-Non-polymers , 1 types, 445 molecules
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 10.0 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Baculovirus expression vector pFastBac1-HM | |||||||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION | |||||||||||||||||||||||||
Virus shell | Name: HRV14-ICAM-1 complex / Diameter: 325 nm / Triangulation number (T number): 3 | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 / Details: PBS | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 420 nm / Calibrated defocus max: 3562 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 83.6 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4680 |
Image scans | Width: 4096 / Height: 4096 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 36638 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12085 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 9.19 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4RHV |