[English] 日本語
Yorodumi
- EMDB-15711: Human rhinovirus 2 empty particle in situ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15711
TitleHuman rhinovirus 2 empty particle in situ
Map dataEM map after pixel size scaling 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: VP3
KeywordsHuman rhinovirus 2 / empty particle / 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: 7.1 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

-
Structure visualization

Supplemental images

emd_15711.png

Downloads & links

-
Map

FileDownload / File: emd_15711.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map after pixel size scaling 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.)
2.65 Å/pix.
x 224 pix.
= 593.116 Å		2.65 Å/pix.
x 224 pix.
= 593.116 Å		2.65 Å/pix.
x 224 pix.
= 593.116 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.64784 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0378
Minimum - Maximum-0.02585645 - 0.07818784
Average (Standard dev.)0.001504892 (±0.0071951663)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 593.11615 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: EM half map before pixel size scaling presented...

Fileemd_15711_half_map_1.map
AnnotationEM half map before pixel size scaling presented in 2-fold on Z (MRC standard) orientation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: EM half map before pixel size scaling presented...

Fileemd_15711_half_map_2.map
AnnotationEM half map before pixel size scaling presented in 2-fold on Z (MRC standard) orientation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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: VP3

-
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: Yes

-
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: 28.851441 KDa
SequenceString: ALDAAETGHT SSVQPEDVIE TRYVQTSQTR DEMSLESFLG RSGCIHESKL EVTLANYNKE NFTVWAINLQ EMAQIRRKFE LFTYTRFDS EITLVPCISA LSQDIGHITM QYMYVPPGAP VPNSRDDYAW QSGTNASVFW QHGQAYPRFS LPFLSVASAY Y MFYDGYDE ...String:
ALDAAETGHT SSVQPEDVIE TRYVQTSQTR DEMSLESFLG RSGCIHESKL EVTLANYNKE NFTVWAINLQ EMAQIRRKFE LFTYTRFDS EITLVPCISA LSQDIGHITM QYMYVPPGAP VPNSRDDYAW QSGTNASVFW QHGQAYPRFS LPFLSVASAY Y MFYDGYDE QDQNYGTANT NNMGSLCSRI VTEKHIHKVH IMTRIYHKAK HVKAWCPRPP RALEYTRAHR TNFKIEDRSI QT AIVTRPI ITTA

UniProtKB: Genome polyprotein

-
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

-
Macromolecule #3: VP3

MacromoleculeName: 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
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) / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 332
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 (ver. 3.0)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 332
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8ay5:
Human rhinovirus 2 empty particle in situ

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more