[English] 日本語
Yorodumi
- EMDB-4903: Echovirus 1 intact particle -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4903
TitleEchovirus 1 intact particle
Map dataE1 control
Sample
  • Virus: Echovirus E1
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
  • Ligand: PALMITIC ACID
KeywordsVIRAL COAT PROTEIN / CAPSID / PICORNAVIRUS / ECHOVIRUS / ICOSAHEDRAL VIRUS / VIRUS
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by 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 / 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 / nucleoside-triphosphate phosphatase ...caveolin-mediated endocytosis of virus by 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 / 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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / host cell cytoplasm / DNA replication / RNA helicase activity / 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 / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / cytoplasm
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
Similarity search - Component
Biological speciesEchovirus E1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDomanska A / Ruokolainen VP
Funding support Finland, 4 items
OrganizationGrant numberCountry
Academy of Finland275199 Finland
Academy of Finland315950 Finland
Sigrid Juselius Foundation Finland
Jane and Aatos Erkko Foundation Finland
CitationJournal: Acta Crystallogr D Biol Crystallogr / Year: 1996
Title: A pseudo-cell based approach to efficient crystallographic refinement of viruses.
Authors: D H Jacobson / J M Hogle / D J Filman /
Abstract: Strategies have been developed for the inexpensive refinement of atomic models of viruses and of other highly symmetric structures. These methods, which have been used in the refinement of several ...Strategies have been developed for the inexpensive refinement of atomic models of viruses and of other highly symmetric structures. These methods, which have been used in the refinement of several strains of poliovirus, focus on an arbitrary-sized parallelepiped (termed the 'protomer' box) containing a single complete averaged copy of the structural motif which forms the protein capsid, together with the fragments of other symmetry-related copies of the motif which are located in its immediate neighborhood. The Fourier transform of the protomer box provides reference structure factors for stereochemically restrained crystallographic refinement of the atomic model parameters. The phases of the reference structure factors are based on the averaged map, and are not permitted to change during the refinement. It is demonstrated that models refined using the protomer box methods do not differ significantly from models refined by more expensive full-cell calculations.
History
DepositionApr 26, 2019-
Header (metadata) releaseJun 12, 2019-
Map releaseJun 12, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6rjf
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rjf
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4903.png

Downloads & links

-
Map

FileDownload / File: emd_4903.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE1 control
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 400 pix.
= 496. Å		1.24 Å/pix.
x 400 pix.
= 496. Å		1.24 Å/pix.
x 400 pix.
= 496. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.05575123 - 0.12277953
Average (Standard dev.)-0.00021832122 (±0.009797896)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 496.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z496.000496.000496.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0560.123-0.000

-
Supplemental data

-
Half map: E1 control half map 2

Fileemd_4903_half_map_1.map
AnnotationE1 control half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: E1 control half map

Fileemd_4903_half_map_2.map
AnnotationE1 control half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Echovirus E1

EntireName: Echovirus E1
Components
  • Virus: Echovirus E1
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
  • Ligand: PALMITIC ACID

-
Supramolecule #1: Echovirus E1

SupramoleculeName: Echovirus E1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 46633 / Sci species name: Echovirus E1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: icosahedral / Diameter: 300.0 Å / T number (triangulation number): 1

-
Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E1 / Strain: Human/Egypt/Farouk/1951
Molecular weightTheoretical: 31.604373 KDa
SequenceString: GDVQNAVEGA MVRVADTVQT SATNSERVPN LTAVETGHTS QAVPGDTMQT RHVINNHVRS ESTIENFLAR SACVFYLEYK TGTKEDSNS FNNWVITTRR VAQLRRKLEM FTYLRFDMEI TVVITSSQDQ STSQNQNAPV LTHQIMYVPP GGPIPVSVDD Y SWQTSTNP ...String:
GDVQNAVEGA MVRVADTVQT SATNSERVPN LTAVETGHTS QAVPGDTMQT RHVINNHVRS ESTIENFLAR SACVFYLEYK TGTKEDSNS FNNWVITTRR VAQLRRKLEM FTYLRFDMEI TVVITSSQDQ STSQNQNAPV LTHQIMYVPP GGPIPVSVDD Y SWQTSTNP SIFWTEGNAP ARMSIPFISI GNAYSNFYDG WSHFSQAGVY GFTTLNNMGQ LFFRHVNKPN PAAITSVARI YF KPKHVRA WVPRPPRLCP YINSTNVNFE PKPVTEVRTN IITT

UniProtKB: Genome polyprotein

-
Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E1
Molecular weightTheoretical: 28.87226 KDa
SequenceString: SPTVEECGYS DRVRSITLGN STITTQECAN VVVGYGEWPE YLSDNEATAE DQPTQPDVAT CRFYTLDSVQ WENGSPGWWW KFPDALRDM GLFGQNMYYH YLGRAGYTIH VQCNASKFHQ GCILVVCVPE AEMGSAQTSG VVNYEHISKG EIASRFTTTT T AEDHGVQA ...String:
SPTVEECGYS DRVRSITLGN STITTQECAN VVVGYGEWPE YLSDNEATAE DQPTQPDVAT CRFYTLDSVQ WENGSPGWWW KFPDALRDM GLFGQNMYYH YLGRAGYTIH VQCNASKFHQ GCILVVCVPE AEMGSAQTSG VVNYEHISKG EIASRFTTTT T AEDHGVQA AVWNAGMGVG VGNLTIFPHQ WINLRTNNSA TIVMPYVNSV PMDNMYRHHN FTLMIIPFVP LDFSAGASTY VP ITVTVAP MCAEYNGLRL AGHQ

UniProtKB: Genome polyprotein

-
Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E1
Molecular weightTheoretical: 26.471074 KDa
SequenceString: GLPTMNTPGS NQFLTSDDFQ SPSAMPQFDV TPEMHIPGEV RNLMEIAEVD SVMPINNDSA AKVSSMEAYR VELSTNTNAG TQVFGFQLN PGAESVMNRT LMGEILNYYA HWSGSIKITF VFCGSAMTTG KFLLSYAPPG AGAPKTRKDA MLGTHVVWDV G LQSSCVLC ...String:
GLPTMNTPGS NQFLTSDDFQ SPSAMPQFDV TPEMHIPGEV RNLMEIAEVD SVMPINNDSA AKVSSMEAYR VELSTNTNAG TQVFGFQLN PGAESVMNRT LMGEILNYYA HWSGSIKITF VFCGSAMTTG KFLLSYAPPG AGAPKTRKDA MLGTHVVWDV G LQSSCVLC IPWISQTHYR FVEKDPYTNA GFVTCWYQTS VVSPASNQPK CYMMCMVSAC NDFSVRMLRD TKFIEQTSFY Q

UniProtKB: Genome polyprotein

-
Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E1
Molecular weightTheoretical: 7.398131 KDa
SequenceString:
GAQVSTQKTG AHETSLSATG NSIIHYTNIN YYKDAASNSA NRQDFTQDPG KFTEPMKDVM IKTLPALN

-
Macromolecule #5: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2 / Details: 2 mM magnesium chloride in PBS
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number real images: 979 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 45309
Startup modelType of model: INSILICO MODEL / In silico model: Used Relion initial model protocol
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 45309
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)

-
Atomic model buiding 1

Initial modelPDB ID:

1ev1


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6rjf:
Echovirus 1 intact particle

-
Atomic model buiding 2

Initial modelPDB ID:

1ev1


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

PDB-6rjf:
Echovirus 1 intact particle

-
Atomic model buiding 3

Initial modelPDB ID:

1ev1


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

PDB-6rjf:
Echovirus 1 intact particle

+
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