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- EMDB-58501: HRV E1007A mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-58501
TitleHRV E1007A mutant
Map data
Sample
  • Virus: rhinovirus B14
    • RNA: RNA (5'-R(P*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
KeywordsCryo-EM / Virus / mutant / 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 / 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
Biological speciesrhinovirus B14
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsMartinez-Romero JM / Caston JR / Mateu MG / Valiente L
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: Riomoros-Barahona V / Martinez-Romero JM / Valiente L / McGrail JP / Gil-Redondo JC / Valbuena A / Caston JR / Mateu MG
History
DepositionJun 11, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58501.png

Downloads & links

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Map

FileDownload / File: emd_58501.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: 0.4
Minimum - Maximum-1.7410039 - 3.1406312
Average (Standard dev.)0.036748692 (±0.22586574)
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: no sharpened map

Fileemd_58501_additional_1.map
Annotationno sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_58501_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_58501_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : rhinovirus B14

EntireName: rhinovirus B14
Components
  • Virus: rhinovirus B14
    • RNA: RNA (5'-R(P*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4

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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: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: 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: 1 / Number of copies: 1
Source (natural)Organism: rhinovirus B14
Molecular weightTheoretical: 4.264403 KDa
SequenceString:
AUUUUUUUUU UUUU

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Macromolecule #2: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rhinovirus B14
Molecular weightTheoretical: 31.917889 KDa
Recombinant expressionOrganism: rhinovirus B14
SequenceString: AEVIVEKTKQ TVASISSGPK HTQKVPILTA NETGATMPVL PSDSIETRTT YMHFNGSETD VECFLGRAAC VHVTEIQNKD ATGIDNHRE AKLFNDWKIN LSSLVQLRKK LELFTYVRFD SEYTILATAS QPDSANYSSN LVVQAMYVPP GAPNPKEWDD Y TWQSASNP ...String:
AEVIVEKTKQ TVASISSGPK HTQKVPILTA NETGATMPVL PSDSIETRTT YMHFNGSETD VECFLGRAAC VHVTEIQNKD ATGIDNHRE AKLFNDWKIN LSSLVQLRKK LELFTYVRFD SEYTILATAS QPDSANYSSN LVVQAMYVPP GAPNPKEWDD Y TWQSASNP SVFFKVGDTS RFSVPYVGLA SAYNCFYDGY SHDDAETQYG ITVLNHMGSM AFRIVNEHDE HKTLVKIRVY HR AKHVEAW IPRAPRALPY TSIGRTNYPK NTEPVIKKRK GDIKSY

UniProtKB: Genome polyprotein

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Macromolecule #3: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: rhinovirus B14
Molecular weightTheoretical: 27.903746 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 MCTEFSG IRSKSIVPQ

UniProtKB: Genome polyprotein

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Macromolecule #4: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 4 / 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 #5: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 5 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
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: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 27097
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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