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- EMDB-50930: Rhinovirus A2 uncoating intermediate revealing the natural pocket... -

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Basic information

Entry
Database: EMDB / ID: EMD-50930
TitleRhinovirus A2 uncoating intermediate revealing the natural pocket factor (pH 5.8 and 4 degrees Celsius)
Map data
Sample
  • Virus: rhinovirus A2
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
  • Ligand: LAURIC ACID
KeywordsUncoating Intermediate / Pocket Factor / Lauric Acid / 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 speciesrhinovirus A2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsReal-Hohn A / Blaas D
Funding support Austria, 1 items
OrganizationGrant numberCountry
Austrian Science FundP31392 Austria
CitationJournal: Sci Rep / Year: 2025
Title: New rhinovirus uncoating intermediate reveals how sodium versus potassium ions influence RNA release.
Authors: Antonio Real-Hohn / Dieter Blaas /
Abstract: Electron microscopy (EM) of rhinovirus A2 (RV-A2) incubated in Na phosphate buffer (pH 7.6) for 12 h at 25 °C revealed partial fragmentation, whereas upon incubation in K phosphate buffer, RV-A2 ...Electron microscopy (EM) of rhinovirus A2 (RV-A2) incubated in Na phosphate buffer (pH 7.6) for 12 h at 25 °C revealed partial fragmentation, whereas upon incubation in K phosphate buffer, RV-A2 appeared intact. In buffers adjusted to pH 5.8, these differences became more pronounced; acidic Na phosphate buffer promoted disintegration of the particles, whereas in acidic K phosphate buffer, the virus appeared like native. Incubation in the acidic buffers for one hour at 4 °C followed by neutralisation resulted in the respective formation of non-infectious A particles (in Na) and a non-infectious novel uncoating intermediate (in K), which we termed 'E0 particle'. Negative staining EM revealed phosphotungstate penetration into A particles, but not into E0 particles. Cryo-EM image reconstruction of the E0 particle showed clear differences between A and E0 particles; like native virus, E0 contained VP4 and a pocket factor. Native RV-A2 RNA cores, obtained by gentle proteinase-K digestion in K and Na phosphate buffer, respectively, differed in accessibility of dsRNA regions, detected by PaSTRy. Variance in RNA compactness observed in K versus Na phosphate buffer was confirmed by rotary shadowing EM; in K phosphate buffer, the RNA remained condensed while, in Na phosphate buffer, distinct unfolding stages were apparent.
History
DepositionJul 7, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50930.png

Downloads & links

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Map

FileDownload / File: emd_50930.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 450 pix.
= 449.1 Å		1 Å/pix.
x 450 pix.
= 449.1 Å		1 Å/pix.
x 450 pix.
= 449.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.998 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.28891322 - 0.4814255
Average (Standard dev.)0.0015118769 (±0.029561857)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 449.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50930_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50930_half_map_2.map
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 A2

EntireName: rhinovirus A2
Components
  • Virus: rhinovirus A2
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
  • Ligand: LAURIC ACID

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Supramolecule #1: rhinovirus A2

SupramoleculeName: rhinovirus A2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 12130 / Sci species name: rhinovirus A2 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Diameter: 310.0 Å / T number (triangulation number): 3

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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 A2
Molecular weightTheoretical: 32.2741 KDa
SequenceString: NPVENYIDEV LNEVLVVPNI NSSNPTTSNS APALDAAETG HTSSVQPEDV IETRYVQTSQ TRDEMSLESF LGRSGCIHES KLEVTLANY NKENFTVWAI NLQEMAQIRR KFELFTYTRF DSEITLVPCI SALSQDIGHI TMQYMYVPPG APVPNSRDDY A WQSGTNAS ...String:
NPVENYIDEV LNEVLVVPNI NSSNPTTSNS APALDAAETG HTSSVQPEDV IETRYVQTSQ TRDEMSLESF LGRSGCIHES KLEVTLANY NKENFTVWAI NLQEMAQIRR KFELFTYTRF DSEITLVPCI SALSQDIGHI TMQYMYVPPG APVPNSRDDY A WQSGTNAS VFWQHGQAYP RFSLPFLSVA SAYYMFYDGY DEQDQNYGTA NTNNMGSLCS RIVTEKHIHK VHIMTRIYHK AK HVKAWCP RPPRALEYTR AHRTNFKIED RSIQTAIVTR PIITTA

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: rhinovirus A2
Molecular weightTheoretical: 29.009588 KDa
SequenceString: SPTVEACGYS DRIIQITRGD STITSQDVAN AIVAYGVWPH YLSSKDASAI DKPSQPDTSS NRFYTLRSVT WSSSSKGWWW KLPDALKDM GIFGENMFYH YLGRSGYTIH VQCNASKFHQ GTLIVALIPE HQIASALHGN VNVGYNYTHP GETGREVKAE T RLNPDLQP ...String:
SPTVEACGYS DRIIQITRGD STITSQDVAN AIVAYGVWPH YLSSKDASAI DKPSQPDTSS NRFYTLRSVT WSSSSKGWWW KLPDALKDM GIFGENMFYH YLGRSGYTIH VQCNASKFHQ GTLIVALIPE HQIASALHGN VNVGYNYTHP GETGREVKAE T RLNPDLQP TEEYWLNFDG TLLGNITIFP HQFINLRSNN SATIIAPYVN AVPMDSMRSH NNWSLVIIPI CPLETSSAIN TI PITISIS PMCAEFSGAR AKRQ

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: rhinovirus A2
Molecular weightTheoretical: 26.107793 KDa
SequenceString: GLPVFITPGS GQFLTTDDFQ SPCALPWYHP TKEISIPGEV KNLVEICQVD SLVPINNTDT YINSENMYSV VLQSSINAPD KIFSIRTDV ASQPLATTLI GEISSYFTHW TGSLRFSFMF CGTANTTVKL LLAYTPPGIA EPTTRKDAML GTHVIWDVGL Q STISMVVP ...String:
GLPVFITPGS GQFLTTDDFQ SPCALPWYHP TKEISIPGEV KNLVEICQVD SLVPINNTDT YINSENMYSV VLQSSINAPD KIFSIRTDV ASQPLATTLI GEISSYFTHW TGSLRFSFMF CGTANTTVKL LLAYTPPGIA EPTTRKDAML GTHVIWDVGL Q STISMVVP WISASHYRNT SPGRSTSGYI TCWYQTRLVI PPQTPPTARL LCFVSGCKDF CLRMARDTNL HLQSGAIAQ

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 A2
Molecular weightTheoretical: 7.356971 KDa
SequenceString:
GAQVSRQNVG THSTQNSVSN GSSLNYFNIN YFKDAASNGA SKLEFTQDPS KFTDPVKDVL EKGIPTLQ

UniProtKB: Genome polyprotein

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Macromolecule #5: LAURIC ACID

MacromoleculeName: LAURIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: DAO
Molecular weightTheoretical: 200.318 Da
Chemical component information

ChemComp-DAO:
LAURIC ACID

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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

Concentration10 mg/mL
BufferpH: 5.8
Component:
ConcentrationFormulaName
0.005841 MK2HPO4Potassium phosphate dibasic
0.09416 MKH2PO4Potassium phosphate monobasic

Details: 0.1 M phosphate buffer, pH 5.8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 293 K / Instrument: LEICA EM GP
DetailsThe virus sample was purified from HeLa cells, diluted to a final concentration of 1 mg/mL in 100 mM potassium phosphate buffer, pH 5.8, and incubated at four degrees for one hour before the vitrification.

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 2 / Number real images: 246 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 100000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 16372
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

10222

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 9825
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 10 / Avg.num./class: 1800 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3vdd


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9g0b:
Rhinovirus A2 uncoating intermediate revealing the natural pocket factor (pH 5.8 and 4 degrees Celsius)

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