[English] 日本語
Yorodumi
- EMDB-0867: Cryo-EM structure of echovirus 11 A-particle at pH 5.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0867
TitleCryo-EM structure of echovirus 11 A-particle at pH 5.5
Map dataNone
Sample
  • Virus: Echovirus E11
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
KeywordsCryo-EM structure / echovirus 11 / A-particle / pH 5.5 / 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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / host cell / nucleoside-triphosphate phosphatase ...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 / viral capsid / host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / host cell cytoplasm / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / 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 / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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 / 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. / 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
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEchovirus E11
Methodsingle particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsLiu S / Gao FG
CitationJournal: Chin.Sci.Bull. / Year: 2020
Title: Molecular and structural basis of Echovirus 11 infection by using the dual-receptor system of CD55 and FcRn.
Authors: Niu S / Liu C / Liu C / Liu S / Song Y / Zhang Y / Tian W / Zhao X / Wang P / Gao FG
History
DepositionNov 13, 2019-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6lb1
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6lb1
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0867.png

Downloads & links

-
Map

FileDownload / File: emd_0867.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 384 pix.
= 418.56 Å		1.09 Å/pix.
x 384 pix.
= 418.56 Å		1.09 Å/pix.
x 384 pix.
= 418.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.05421064 - 0.13915934
Average (Standard dev.)0.0005849376 (±0.010819978)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 418.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z418.560418.560418.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0540.1390.001

-
Supplemental data

-
Sample components

-
Entire : Echovirus E11

EntireName: Echovirus E11
Components
  • Virus: Echovirus E11
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3

-
Supramolecule #1: Echovirus E11

SupramoleculeName: Echovirus E11 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12078 / Sci species name: Echovirus E11 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

-
Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E11
Molecular weightTheoretical: 26.048557 KDa
SequenceString: SESSIENFLC RSACVYMGEY HTTNTDTSKL FASWTINARR MVQMRRKLEL FTYVRFDMEV TFVITSKQDQ GTQLGQDMPP LTHQIMYIP PGGPIPKSVT DYTWQTSTNP SIFWTEGNAP PRMSIPFISI GNAYSNFYDG WSHFSQNGVY GYNTLNHMGQ I YVRHVNGS ...String:
SESSIENFLC RSACVYMGEY HTTNTDTSKL FASWTINARR MVQMRRKLEL FTYVRFDMEV TFVITSKQDQ GTQLGQDMPP LTHQIMYIP PGGPIPKSVT DYTWQTSTNP SIFWTEGNAP PRMSIPFISI GNAYSNFYDG WSHFSQNGVY GYNTLNHMGQ I YVRHVNGS SPLPMTSTVR MYFKPKHVKV WVPRPPRLCQ YKNASTVNFT PTNITEKRQS INYIPETV

-
Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E11
Molecular weightTheoretical: 27.367783 KDa
SequenceString: RVRSITLGNS TITTQESANV VVAYGRWPEY LKDNEATAED QPTQPDVATC RFYTLESVTW ERDSPGWWWK FPDALKDMGL FGQNMYYHY LGRAGYTIHV QCNASKFHQG CLMVVCVPEA EMGCSQVDGT VNEHSLSEGE TAKKFASTST NGTNTVQSIV T NAGMGVGV ...String:
RVRSITLGNS TITTQESANV VVAYGRWPEY LKDNEATAED QPTQPDVATC RFYTLESVTW ERDSPGWWWK FPDALKDMGL FGQNMYYHY LGRAGYTIHV QCNASKFHQG CLMVVCVPEA EMGCSQVDGT VNEHSLSEGE TAKKFASTST NGTNTVQSIV T NAGMGVGV GNLTIFPHQW INLRTNNCAT IVMPYINNVP MDNMFRHHNF TLMIIPFVPL DYSSDSSTYV PITVTVAPMC AE YNGLR

-
Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E11
Molecular weightTheoretical: 25.29273 KDa
SequenceString: GLPVMNTPGS NQFLTSDDFQ SPSAMPQFDV TPELNIPGEV QNLMEIAEVD SVVPVNNVEG KLDTMEIYRI PVQSGNHQSS QVFGFQVQP GLDNVFKHTL LGEILNYYAH WSGSIKLTFV FCGSAMATGK FLLAYAPPGA NAPKSRKDAM LGTHIIWDVG L QSSCVLCI ...String:
GLPVMNTPGS NQFLTSDDFQ SPSAMPQFDV TPELNIPGEV QNLMEIAEVD SVVPVNNVEG KLDTMEIYRI PVQSGNHQSS QVFGFQVQP GLDNVFKHTL LGEILNYYAH WSGSIKLTFV FCGSAMATGK FLLAYAPPGA NAPKSRKDAM LGTHIIWDVG L QSSCVLCI PWISQTHYRL VQQDEYTSAG NVTCWYQTGI VVPAGTPTSC SIMCFVSACN DFSVRLLKDT PFI

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 5.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.025 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75452
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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