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- PDB-9g0b: Rhinovirus A2 uncoating intermediate revealing the natural pocket... -

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Basic information

Entry
Database: PDB / ID: 9g0b
TitleRhinovirus A2 uncoating intermediate revealing the natural pocket factor (pH 5.8 and 4 degrees Celsius)
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
  • Capsid protein VP4
KeywordsVIRUS / Uncoating Intermediate / Pocket Factor / Lauric Acid
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase 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 / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase 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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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
LAURIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesrhinovirus A2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsReal-Hohn, A. / Blaas, D.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP31392 Austria
CitationJournal: Sci Rep / Year: 2025
Title: New rhinovirus uncoating intermediate reveals how sodium versus potassium ions influence RNA release.
Authors: Antonio Real-Hohn / Dieter Blaas /
Abstract: Electron microscopy (EM) of rhinovirus A2 (RV-A2) incubated in Na phosphate buffer (pH 7.6) for 12 h at 25 °C revealed partial fragmentation, whereas upon incubation in K phosphate buffer, RV-A2 ...Electron microscopy (EM) of rhinovirus A2 (RV-A2) incubated in Na phosphate buffer (pH 7.6) for 12 h at 25 °C revealed partial fragmentation, whereas upon incubation in K phosphate buffer, RV-A2 appeared intact. In buffers adjusted to pH 5.8, these differences became more pronounced; acidic Na phosphate buffer promoted disintegration of the particles, whereas in acidic K phosphate buffer, the virus appeared like native. Incubation in the acidic buffers for one hour at 4 °C followed by neutralisation resulted in the respective formation of non-infectious A particles (in Na) and a non-infectious novel uncoating intermediate (in K), which we termed 'E0 particle'. Negative staining EM revealed phosphotungstate penetration into A particles, but not into E0 particles. Cryo-EM image reconstruction of the E0 particle showed clear differences between A and E0 particles; like native virus, E0 contained VP4 and a pocket factor. Native RV-A2 RNA cores, obtained by gentle proteinase-K digestion in K and Na phosphate buffer, respectively, differed in accessibility of dsRNA regions, detected by PaSTRy. Variance in RNA compactness observed in K versus Na phosphate buffer was confirmed by rotary shadowing EM; in K phosphate buffer, the RNA remained condensed while, in Na phosphate buffer, distinct unfolding stages were apparent.
History
DepositionJul 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9495
Polymers94,7484
Non-polymers2001
Water00
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,696,926300
Polymers5,684,907240
Non-polymers12,01960
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

#1: Protein Capsid protein VP1 / P1D / Virion protein 1


Mass: 32274.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) rhinovirus A2 / References: UniProt: P04936
#2: Protein Capsid protein VP2 / P1B / Virion protein 2


Mass: 29009.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) rhinovirus A2 / References: UniProt: P04936
#3: Protein Capsid protein VP3 / P1C / Virion protein 3


Mass: 26107.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) rhinovirus A2 / References: UniProt: P04936
#4: Protein Capsid protein VP4 / P1A / Virion protein 4


Mass: 7356.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) rhinovirus A2 / References: UniProt: P04936
#5: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: rhinovirus A2 / Type: VIRUS / Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: rhinovirus A2
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 310 nm / Triangulation number (T number): 3
Buffer solutionpH: 5.8 / Details: 0.1 M phosphate buffer, pH 5.8
Buffer component
IDConc.NameFormulaBuffer-ID
10.005841 MPotassium phosphate dibasicK2HPO41
20.09416 MPotassium phosphate monobasicKH2PO41
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The virus sample was purified from HeLa cells, diluted to a final concentration of 1 mg/mL in 100 mM potassium phosphate buffer, pH 5.8, and incubated at four degrees for one hour before the vitrification.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 293 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 100000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 246

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2EPU3image acquisition
4CTFFIND4.1CTF correction
7UCSF Chimera1.17.2model fitting
8Coot0.9model fitting
9PHENIX1.21model fitting
11RELION4initial Euler assignment
12RELION4final Euler assignment
13RELION4classification
14RELION43D reconstruction
15Coot0.9model refinement
16PHENIX1.21model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 16372
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9825 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 3VDD

3vdd


Accession code: 3VDD / Source name: PDB / Type: experimental model

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