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- EMDB-4903: Echovirus 1 intact particle -

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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
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 ...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 / protein complex oligomerization / monoatomic ion channel activity / host cell cytoplasm / 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 / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / 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) / 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. / 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
Capsid protein VP0 / Genome polyprotein
Similarity search - Component
Biological speciesE-1 (virus) / Echovirus E1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDomanska A / Ruokolainen VP / Pelliccia M / Laajala MA / Marjomaki VS / Butcher SJ
Funding support Finland, 4 items
OrganizationGrant numberCountry
Academy of Finland275199 Finland
Sigrid Juselius Foundation Finland
Academy of Finland315950 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-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

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

emd_4903.png

Downloads & links

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Map

FileDownload / File: emd_4903.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE1 control
Voxel sizeX=Y=Z: 1.24 Å
Density
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

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Supplemental data

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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)

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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)

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Sample components

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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

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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

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: E-1 (virus) / 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

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: E-1 (virus)
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

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: E-1 (virus)
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

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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

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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 / Palmitic 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

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

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Electron microscopy

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

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Image processing

Particle selectionNumber selected: 45309
CTF correctionSoftware - Name: Gctf
Startup modelType of model: INSILICO MODEL / In silico model: Used Relion initial model protocol
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
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

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Atomic model buiding 1

Initial modelPDB ID:

1ev1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6rjf:
Echovirus 1 intact particle

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Atomic model buiding 2

Initial modelPDB ID:

1ev1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6rjf:
Echovirus 1 intact particle

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Atomic model buiding 3

Initial modelPDB ID:

1ev1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6rjf:
Echovirus 1 intact particle

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