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- PDB-31lf: HRV virion E2250A mutant -

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Basic information

Entry
Database: PDB / ID: 31lf
TitleHRV virion E2250A mutant
Components
  • Capsid protein VP1
  • Capsid protein VP3
  • Capsid protein VP4
  • Genome polyprotein
  • RNA (5'-R(P*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsVIRUS / Cryoem / HRV / mutant
Function / homology
Function and homology information


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 / ribonucleoside triphosphate phosphatase activity / 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 / ribonucleoside triphosphate phosphatase activity / 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 / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / DNA-templated transcription / RNA binding / zinc ion binding / ATP 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RdRp of positive ssRNA viruses catalytic domain profile. / RNA-directed RNA polymerase, catalytic domain / 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
RNA / RNA (> 10) / : / Genome polyprotein
Similarity search - Component
Biological speciesrhinovirus B14
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsMartinez-Romero, J.M. / Caston, J.R. / Mateu, M.G.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: J.Mol.Biol. / Year: 2026
Title: RNA-repelling Anionic Clusters in Human Rhinovirus Cooperate with Cationic Residues to Promote Virion Assembly and Restrain RNA Release
Authors: Riomoros-Barahona, V. / Martinez-Romero, J.M. / Valiente, L. / McGrail, J.P. / Gil-Redondo, J.C. / Valbuena, A. / Caston, J.R. / Mateu, M.G.
History
DepositionJun 11, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Capsid protein VP1
2: Genome polyprotein
3: Capsid protein VP3
4: Capsid protein VP4
5: RNA (5'-R(P*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)95,2875
Polymers95,2875
Non-polymers00
Water00
1
1: Capsid protein VP1
2: Genome polyprotein
3: Capsid protein VP3
4: Capsid protein VP4
5: RNA (5'-R(P*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
x 60


Theoretical massNumber of molelcules
Total (without water)5,717,240300
Polymers5,717,240300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

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


Mass: 31846.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) rhinovirus B14 / Production host: rhinovirus B14 / References: UniProt: P03303
#2: Protein Genome polyprotein


Mass: 27845.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) rhinovirus B14 / Production host: rhinovirus B14 / References: UniProt: A0A5B9MV00
#3: Protein Capsid protein VP3


Mass: 26236.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) rhinovirus B14 / Production host: rhinovirus B14 / References: UniProt: P03303
#4: Protein/peptide Capsid protein VP4 / P1A / Virion protein 4


Mass: 5093.653 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) rhinovirus B14 / Production host: rhinovirus B14 / References: UniProt: P03303
#5: RNA chain RNA (5'-R(P*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 4264.403 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) rhinovirus B14 / Production host: rhinovirus B14
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 B14 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: rhinovirus B14
Source (recombinant)Organism: rhinovirus B14
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17316 / Symmetry type: POINT
Atomic model buildingSource name: PDB / Type: experimental model

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