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- PDB-29ti: HRV K4058A mutant -

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Basic information

Entry
Database: PDB / ID: 29ti
TitleHRV K4058A mutant
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
  • Capsid protein VP4
KeywordsVIRUS / Cryoem / virion / HRV
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 / DNA-templated transcription / proteolysis / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / 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
Biological speciesrhinovirus B14
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsMartinez-Romero, J.M. / Caston, J.R. / Mauricio, M.G.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: J Mol Biol / Year: 2026
Title: Biologically Relevant, Cationic Residues in Human Rhinovirus Stabilize Capsid-Bound RNA Duplexes, and Restrict Capsid Flexibility.
Authors: Juan M Martínez-Romero / Luis Valiente / José Luis Vilas / Valentín Riomoros-Barahona / Alejandro Valbuena / Mauricio G Mateu / José R Castón /
Abstract: Human rhinoviruses (RV) cause severe socioeconomic problems and are also associated to, or exacerbate, severe respiratory diseases, but no anti-RV drugs are available so far. Understanding the ...Human rhinoviruses (RV) cause severe socioeconomic problems and are also associated to, or exacerbate, severe respiratory diseases, but no anti-RV drugs are available so far. Understanding the functional role(s) of capsid-RNA interactions in the RV virion may contribute to antiviral drug development. Our previous studies showed that the genome inside the RV-B14 virion is organized as a capsid-bound RNA dodecahedral cage formed by 30 intrachain RNA duplexes; and that positively charged capsid residues close to each RNA duplex, including K4058 and K2052, are involved in viral infection by promoting virion assembly and controlling genome uncoating. In this study, cryogenic electron microscopy was used to investigate the structural basis that underlies the functional roles of those positively charged residues in the RV virion. The atomic structure and equilibrium conformation dynamics of mutant virions carrying either K4058A or K2052A substitutions were compared with those of the parental RV-B14 virion under identical conditions. The results showed that both K4058 and K2052 residues stabilize the RNA duplex structure, and modulate capsid conformation and equilibrium dynamics. Notably, the partially disorganized RNA elements in the K4058A mutant virion strongly resemble those previously found by other researchers in an alternative wild-type RV-B14 structure. Comparison of the two alternative wild-type virion structures and the mutant virion structures supports the existence of two conformational states of the RV virion in the absence of cell receptor: a basal state with well-structured RNA duplexes, and an activated, RNA release-prone state in which the RNA duplexes are partially disorganized.
History
DepositionApr 7, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)89,9954
Polymers89,9954
Non-polymers00
Water00
1
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,399,684240
Polymers5,399,684240
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: 31147.984 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 Capsid protein VP2 / P1B / Virion protein 2


Mass: 27903.746 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
#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: 4706.242 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
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
Virus shellDiameter: 300 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 95 %

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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: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63778 / Symmetry type: POINT
RefinementHighest resolution: 3.26 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00639000
ELECTRON MICROSCOPYf_angle_d1.07153226
ELECTRON MICROSCOPYf_dihedral_angle_d5.8665244
ELECTRON MICROSCOPYf_chiral_restr0.0616072
ELECTRON MICROSCOPYf_plane_restr0.016816

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