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- EMDB-15710: Human rhinovirus 2 virion in situ -

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Basic information

Entry
Database: EMDB / ID: EMD-15710
TitleHuman rhinovirus 2 virion in situ
Map dataPixel size scaled EM map presented in 2-fold on Z (MRC standard) orientation. Micrographs were collected on lamellipodia of Cos7 cells infected with HRV2.
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
KeywordsHuman rhinovirus 2 / in situ / cryo-EM. / VIRUS
Function / homology
Function and homology information


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 / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis 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 / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
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) / Picornavirales 3C/3C-like protease domain ...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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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: 4.7 Å
AuthorsIshemgulova A / Mukhamedova L / Trebichalska Z / Payne P / Smerdova L / Moravcova J / Hrebik D / Buchta D / Skubnik K / Fuzik T ...Ishemgulova A / Mukhamedova L / Trebichalska Z / Payne P / Smerdova L / Moravcova J / Hrebik D / Buchta D / Skubnik K / Fuzik T / Novacek J / Plevka P
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Czech Science FoundationGX19-25982X Czech Republic
CitationJournal: To Be Published
Title: Endosome rupture enables enteroviruses to infect cells.
Authors: Ishemgulova A
History
DepositionSep 1, 2022-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateSep 13, 2023-
Current statusSep 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15710.png

Downloads & links

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Map

FileDownload / File: emd_15710.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPixel size scaled EM map presented in 2-fold on Z (MRC standard) orientation. Micrographs were collected on lamellipodia of Cos7 cells infected with HRV2.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 448 pix.
= 593.116 Å		1.32 Å/pix.
x 448 pix.
= 593.116 Å		1.32 Å/pix.
x 448 pix.
= 593.116 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32392 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0135
Minimum - Maximum-0.018463194 - 0.034436252
Average (Standard dev.)0.0006287712 (±0.0026698448)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 593.11615 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM map presented in 2-fold on Z (MRC standard) orientation.

Fileemd_15710_half_map_1.map
AnnotationEM map presented in 2-fold on Z (MRC standard) orientation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM map presented in 2-fold on Z (MRC standard) orientation.

Fileemd_15710_half_map_2.map
AnnotationEM map presented in 2-fold on Z (MRC standard) orientation.
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

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Supramolecule #1: rhinovirus A2

SupramoleculeName: rhinovirus A2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12130 / Sci species name: rhinovirus A2 / Virus type: VIRION / Virus isolate: OTHER / 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 A2
Molecular weightTheoretical: 30.645367 KDa
SequenceString: LVVPNINSSN PTTSNSAPAL DAAETGHTSS VQPEDVIETR YVQTSQTRDE MSLESFLGRS GCIHESKLEV TLANYNKENF TVWAINLQE MAQIRRKFEL FTYTRFDSEI TLVPCISALS QDIGHITMQY MYVPPGAPVP NSRDDYAWQS GTNASVFWQH G QAYPRFSL ...String:
LVVPNINSSN PTTSNSAPAL DAAETGHTSS VQPEDVIETR YVQTSQTRDE MSLESFLGRS GCIHESKLEV TLANYNKENF TVWAINLQE MAQIRRKFEL FTYTRFDSEI TLVPCISALS QDIGHITMQY MYVPPGAPVP NSRDDYAWQS GTNASVFWQH G QAYPRFSL PFLSVASAYY MFYDGYDEQD QNYGTANTNN MGSLCSRIVT EKHIHKVHIM TRIYHKAKHV KAWCPRPPRA LE YTRAHRT NFKIEDRSIQ TAIVTRPIIT TA

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: 27.899426 KDa
SequenceString: RIIQITRGDS TITSQDVANA IVAYGVWPHY LSSKDASAID KPSQPDTSSN RFYTLRSVTW SSSSKGWWWK LPDALKDMGI FGENMFYHY LGRSGYTIHV QCNASKFHQG TLIVALIPEH QIASALHGNV NVGYNYTHPG ETGREVKAET RLNPDLQPTE E YWLNFDGT ...String:
RIIQITRGDS TITSQDVANA IVAYGVWPHY LSSKDASAID KPSQPDTSSN RFYTLRSVTW SSSSKGWWWK LPDALKDMGI FGENMFYHY LGRSGYTIHV QCNASKFHQG TLIVALIPEH QIASALHGNV NVGYNYTHPG ETGREVKAET RLNPDLQPTE E YWLNFDGT LLGNITIFPH QFINLRSNNS ATIIAPYVNA VPMDSMRSHN NWSLVIIPIC PLETSSAINT IPITISISPM CA EFSGARA KRQ

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: 2.810063 KDa
SequenceString:
AQVSRQNYFN INYFKDAASN GASKL

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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: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Digitization - Frames/image: 1-40 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1590 / Details: Particles were picked manually.
Startup modelType of model: OTHER / Details: AB INITIO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION / Details: RELION SGD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 1424
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1fpn

chain_id: 1

1fpn

chain_id: 2

1fpn

chain_id: 3

1fpn

chain_id: 4
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8ay4:
Human rhinovirus 2 virion in situ

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