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- EMDB-58502: HRV virion E2250A mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-58502
TitleHRV virion E2250A mutant
Map data
Sample
  • Virus: rhinovirus B14
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
    • RNA: RNA (5'-R(P*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsCryoem / Virus / 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 / nucleoside-triphosphate phosphatase / ribonucleoside triphosphate phosphatase activity ...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 / nucleoside-triphosphate phosphatase / ribonucleoside triphosphate phosphatase activity / 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 / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell cytoplasm / virion attachment to host cell / host cell nucleus / structural molecule activity / 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 / 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 / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Genome polyprotein
Similarity search - Component
Biological speciesrhinovirus B14
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsMartinez-Romero JM / Caston JR / Mateu MG
Funding support Spain, 1 items
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: Valentín Riomoros-Barahona / Juan M Martínez-Romero / Luis Valiente / Joseph Patrick McGrail / Juan Carlos Gil-Redondo / Alejandro Valbuena / José R Castón / Mauricio G Mateu /
Abstract: Research on virus nucleic acid-protein interactions is important to understand infection and guide antiviral drug design. In previous studies we showed that the human rhinovirus (RV) genomic RNA is ...Research on virus nucleic acid-protein interactions is important to understand infection and guide antiviral drug design. In previous studies we showed that the human rhinovirus (RV) genomic RNA is organized as a dodecahedral cage formed by 30 RNA duplex elements anchored to capsid concavities. We showed also that capsid-RNA duplex interactions include conserved tryptophans, neutral polar residues, and many positively charged residues that promote virion assembly and restrain RNA release by stabilizing the negatively charged RNA duplex structure. The present study expands our understanding of the capsid-RNA duplex interface in RV by addressing the structural and functional roles of conserved patches of negatively charged capsid residues interposed between each RNA duplex and its binding site at the capsid inner surface. The initial hypothesis was that electrostatic repulsion between anionic residues and RNA phosphates would lead to functional effects opposite to those previously found for cationic residues that can electrostatically attract RNA phosphates. In fact, those anionic residues do not oppose, but act together with cationic residues at the RNA duplex binding sites to promote virion assembly and restrain RNA release. Cryogenic electron microscopy analysis showed that negatively charged residues at the capsid-RNA duplex interfaces have a different structural role than positively charged residues, even though they all play similar functional roles. A tentative model is discussed to explain the functional effects of the complex distribution of negative and positive electrostatic potential found at capsid-RNA duplex interfaces in RV.
History
DepositionJun 11, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58502.png

Downloads & links

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Map

FileDownload / File: emd_58502.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 480 pix.
= 403.2 Å		0.84 Å/pix.
x 480 pix.
= 403.2 Å		0.84 Å/pix.
x 480 pix.
= 403.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-1.4121374 - 2.4224725
Average (Standard dev.)0.037155394 (±0.18289018)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 403.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_58502_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_58502_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_58502_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : rhinovirus B14

EntireName: rhinovirus B14
Components
  • Virus: rhinovirus B14
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
    • RNA: RNA (5'-R(P*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')

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Supramolecule #1: rhinovirus B14

SupramoleculeName: rhinovirus B14 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12131 / Sci species name: rhinovirus B14 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rhinovirus B14
Molecular weightTheoretical: 31.846811 KDa
Recombinant expressionOrganism: rhinovirus B14
SequenceString: EVIVEKTKQT VASISSGPKH TQKVPILTAN ETGATMPVLP SDSIETRTTY MHFNGSETDV ECFLGRAACV HVTEIQNKDA TGIDNHREA KLFNDWKINL SSLVQLRKKL ELFTYVRFDS EYTILATASQ PDSANYSSNL VVQAMYVPPG APNPKEWDDY T WQSASNPS ...String:
EVIVEKTKQT VASISSGPKH TQKVPILTAN ETGATMPVLP SDSIETRTTY MHFNGSETDV ECFLGRAACV HVTEIQNKDA TGIDNHREA KLFNDWKINL SSLVQLRKKL ELFTYVRFDS EYTILATASQ PDSANYSSNL VVQAMYVPPG APNPKEWDDY T WQSASNPS VFFKVGDTSR FSVPYVGLAS AYNCFYDGYS HDDAETQYGI TVLNHMGSMA FRIVNEHDEH KTLVKIRVYH RA KHVEAWI PRAPRALPYT SIGRTNYPKN TEPVIKKRKG DIKSY

UniProtKB: Genome polyprotein

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Macromolecule #2: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rhinovirus B14
Molecular weightTheoretical: 27.845711 KDa
Recombinant expressionOrganism: rhinovirus B14
SequenceString: CGYSDRVQQI TLGNSTITTQ EAANAVVCYA EWPEYLPDVD ASDVNKTSKP DTSVCRFYTL DSKTWTTGSK GWCWKLPDAL KDMGVFGQN MFFHSLGRSG YTVHVQCNAT KFHSGCLLVV VIPEHQLASH EGGNVSVKYT FTHPGERGID LSSANEVGGP V KDVLYNMN ...String:
CGYSDRVQQI TLGNSTITTQ EAANAVVCYA EWPEYLPDVD ASDVNKTSKP DTSVCRFYTL DSKTWTTGSK GWCWKLPDAL KDMGVFGQN MFFHSLGRSG YTVHVQCNAT KFHSGCLLVV VIPEHQLASH EGGNVSVKYT FTHPGERGID LSSANEVGGP V KDVLYNMN GTLLGNLLIF PHQFINLRTN NTATIVIPYI NSVPIDSMTR HNNVSLMVIP IAPLTVPTGA TPSLPITVTI AP MCTAFSG IRSKSIVPQ

UniProtKB: UNIPROTKB: A0A5B9MV00

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Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rhinovirus B14
Molecular weightTheoretical: 26.236754 KDa
Recombinant expressionOrganism: rhinovirus B14
SequenceString: GLPTTTLPGS GQFLTTDDRQ SPSALPNYEP TPRIHIPGKV HNLLEIIQVD TLIPMNNTHT KDEVNSYLIP LNANRQNEQV FGTNLFIGD GVFKTTLLGE IVQYYTHWSG SLRFSLMYTG PALSSAKLIL AYTPPGARGP QDRREAMLGT HVVWDIGLQS T IVMTIPWT ...String:
GLPTTTLPGS GQFLTTDDRQ SPSALPNYEP TPRIHIPGKV HNLLEIIQVD TLIPMNNTHT KDEVNSYLIP LNANRQNEQV FGTNLFIGD GVFKTTLLGE IVQYYTHWSG SLRFSLMYTG PALSSAKLIL AYTPPGARGP QDRREAMLGT HVVWDIGLQS T IVMTIPWT SGVQFRYTDP DTYTSAGFLS CWYQTSLILP PETTGQVYLL SFISACPDFK LRLMKDTQTI SQTVALTE

UniProtKB: Genome polyprotein

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Macromolecule #4: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rhinovirus B14
Molecular weightTheoretical: 5.093653 KDa
Recombinant expressionOrganism: rhinovirus B14
SequenceString:
SNQTFTYINY YKDAASTSSA GQSLSMDPSK FTEPVKDLML KGAPALN

UniProtKB: Genome polyprotein

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Macromolecule #5: RNA (5'-R(P*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: rhinovirus B14
Molecular weightTheoretical: 4.264403 KDa
SequenceString:
AUUUUUUUUU UUUU

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 17316
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-31lf:
HRV virion E2250A mutant

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