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- EMDB-50844: CryoEM structure of RV-A89 -

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Basic information

Entry
Database: EMDB / ID: EMD-50844
TitleCryoEM structure of RV-A89
Map dataCryoEm structure of RV-A89 [empty]
Sample
  • Virus: Human rhinovirus 89 ATCC VR-1199
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
KeywordsRV-A89 / rhinovirus / VIRUS
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
Biological speciesHuman rhinovirus 89 ATCC VR-1199
Methodsingle particle reconstruction / cryo EM / Resolution: 1.96 Å
AuthorsWald J / Blaas D / Marlovits TC
Funding support Germany, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST152/772-1 Germany
German Research Foundation (DFG)152/774-1 Germany
German Research Foundation (DFG)152/775-1 Germany
German Research Foundation (DFG)152/776-1 Germany
German Research Foundation (DFG)152/777-1 Germany
CitationJournal: Sci Rep / Year: 2024
Title: DMSO might impact ligand binding, capsid stability, and RNA interaction in viral preparations.
Authors: Jiri Wald / Nikolaus Goessweiner-Mohr / Antonio Real-Hohn / Dieter Blaas / Thomas C Marlovits /
Abstract: Dimethyl sulfoxide (DMSO) is a widely used solvent in drug research. However, recent studies indicate that even at low concentration DMSO might cause structural changes of proteins and RNA. The ...Dimethyl sulfoxide (DMSO) is a widely used solvent in drug research. However, recent studies indicate that even at low concentration DMSO might cause structural changes of proteins and RNA. The pyrazolopyrimidine antiviral OBR-5-340 dissolved in DMSO inhibits rhinovirus-B5 infection yet is inactive against RV-A89. This is consistent with our structural observation that OBR-5-340 is only visible at the pocket factor site in rhinovirus-B5 and not in RV-A89, where the hydrophobic pocket is collapsed. Here, we analyze the impact of DMSO in RV-A89 by high-resolution cryo-electron microscopy. Our 1.76 Å cryo-EM reconstruction of RV-A89 in plain buffer, without DMSO, reveals that the pocket-factor binding site is occupied by myristate and that the previously observed local heterogeneity at protein-RNA interfaces is absent. These findings suggest that DMSO elutes the pocket factor, leading to a collapse of the hydrophobic pocket of RV-A89. Consequently, the conformational heterogeneity observed at the RNA-protein interface in the presence of DMSO likely results from increased capsid flexibility due to the absence of the pocket factor and DMSO-induced affinity modifications. This local asymmetry may promote a directional release of the RNA genome during infection.
History
DepositionJul 2, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50844.png

Downloads & links

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Map

FileDownload / File: emd_50844.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEm structure of RV-A89 [empty]
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.41 Å/pix.
x 1000 pix.
= 413.019 Å		0.41 Å/pix.
x 1000 pix.
= 413.019 Å		0.41 Å/pix.
x 1000 pix.
= 413.019 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.41302 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.151
Minimum - Maximum-0.55189556 - 1.060366
Average (Standard dev.)0.0034571865 (±0.05011227)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100010001000
Spacing100010001000
CellA=B=C: 413.019 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50844_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap 1

Fileemd_50844_half_map_1.map
Annotationhalfmap_1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap 2

Fileemd_50844_half_map_2.map
Annotationhalfmap_2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human rhinovirus 89 ATCC VR-1199

EntireName: Human rhinovirus 89 ATCC VR-1199
Components
  • Virus: Human rhinovirus 89 ATCC VR-1199
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3

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Supramolecule #1: Human rhinovirus 89 ATCC VR-1199

SupramoleculeName: Human rhinovirus 89 ATCC VR-1199 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 650130 / Sci species name: Human rhinovirus 89 ATCC VR-1199 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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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: Human rhinovirus 89 ATCC VR-1199
Molecular weightTheoretical: 23.982973 KDa
Recombinant expressionOrganism: Human rhinovirus 89 ATCC VR-1199
SequenceString: TRDETSIESF LGRSGCIAMI EFNTSSDKTE HDKIGKGFKT WKVSLQEMAQ IRRKYELFTY TRFDSEITIV TAAAAQGNDS GHIVLQFMY VPPGAPVPEK RDDYTWQSGT NASVFWQEGQ PYPRFTIPFM SIASAYYMFY DGYDGDSAAS KYGSVVTNDM G TICVRIVT ...String:
TRDETSIESF LGRSGCIAMI EFNTSSDKTE HDKIGKGFKT WKVSLQEMAQ IRRKYELFTY TRFDSEITIV TAAAAQGNDS GHIVLQFMY VPPGAPVPEK RDDYTWQSGT NASVFWQEGQ PYPRFTIPFM SIASAYYMFY DGYDGDSAAS KYGSVVTNDM G TICVRIVT SNQKHDSNIV CRIYHKAKHI KAWCPRPPRA VAYQHTHSTN YIP

UniProtKB: Genome polyprotein

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Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human rhinovirus 89 ATCC VR-1199
Molecular weightTheoretical: 27.150258 KDa
Recombinant expressionOrganism: Human rhinovirus 89 ATCC VR-1199
SequenceString: IQITRGDSTI TSQDTANAVV AYGVWPSYLT PDDATAIDKP TQPDTSSNRF YTLDSRSWTS ASSGWWWKLP DALKNMGIFG ENMFYHFLG RSGYTIHVQC NSSKFHQGLL IVAAIPEHQL ASATSGNVSV GYNHTHPGEQ GREVVPSRTS SDNKRPSDDS W LNFDGTLL ...String:
IQITRGDSTI TSQDTANAVV AYGVWPSYLT PDDATAIDKP TQPDTSSNRF YTLDSRSWTS ASSGWWWKLP DALKNMGIFG ENMFYHFLG RSGYTIHVQC NSSKFHQGLL IVAAIPEHQL ASATSGNVSV GYNHTHPGEQ GREVVPSRTS SDNKRPSDDS W LNFDGTLL GNLPIYPHQY INLRTNNSAT LILPYVNAVP MDSMLRHNNW SLVIIPICPL QVQPGGTQSI PITVSISPMF SE FSGPRS

UniProtKB: Genome polyprotein

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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: Human rhinovirus 89 ATCC VR-1199
Molecular weightTheoretical: 25.399967 KDa
Recombinant expressionOrganism: Human rhinovirus 89 ATCC VR-1199
SequenceString: PVMLTPGSGQ FLTTDDTQSP SAFPYFHPTK EIFIPGQVRN LIEMCQVDTL IPVNNTQENV RSVNMYTVDL RTQVDLAKEV FSIPVDIAS QPLATTLIGE LASYYTHWTG SLRFSFMFCG SASSTLKLLI AYTPPGVGKP KSRREAMLGT HLVWDVGLQS T ASLVVPWV ...String:
PVMLTPGSGQ FLTTDDTQSP SAFPYFHPTK EIFIPGQVRN LIEMCQVDTL IPVNNTQENV RSVNMYTVDL RTQVDLAKEV FSIPVDIAS QPLATTLIGE LASYYTHWTG SLRFSFMFCG SASSTLKLLI AYTPPGVGKP KSRREAMLGT HLVWDVGLQS T ASLVVPWV SASHFRFTTP DTYSSAGYIT CWYQTNFVVP DSTPDNAKMV CMVSACKDFC LRLARDTNLH T

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: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4860 / Average exposure time: 2.0 sec. / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 27000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-9fx9:
CryoEM structure of RV-A89

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