+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4903 | |||||||||||||||
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Title | Echovirus 1 intact particle | |||||||||||||||
Map data | E1 control | |||||||||||||||
Sample |
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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 / DNA replication / RNA helicase activity / 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 | |||||||||||||||
Biological species | E-1 (virus) / Echovirus E1 | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Domanska A / Ruokolainen VP / Pelliccia M / Laajala MA / Marjomaki VS / Butcher SJ | |||||||||||||||
Funding support | Finland, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4903.map.gz | 221.2 MB | EMDB map data format | |
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Header (meta data) | emd-4903-v30.xml emd-4903.xml | 22.8 KB 22.8 KB | Display Display | EMDB header |
Images | emd_4903.png | 134.8 KB | ||
Others | emd_4903_half_map_1.map.gz emd_4903_half_map_2.map.gz | 192.1 MB 192.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4903 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4903 | HTTPS FTP |
-Related structure data
Related structure data | 6rjfMC 0565C 6o06C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10284 (Title: Extracellular albumin and endosomal ions prime enterovirus particles for uncoating that can be prevented by fatty acid saturation Data size: 2.4 TB Data #1: Unaligned multi-frame micrographs of control Echovirus 1 [micrographs - multiframe] Data #2: Unaligned multi-frame micrographs of control Echovirus 1 [micrographs - multiframe] Data #3: Unaligned multi-frame micrographs of treated Echovirus 1 (expanded particle) [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4903.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | E1 control | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: E1 control half map 2
File | emd_4903_half_map_1.map | ||||||||||||
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Annotation | E1 control half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: E1 control half map
File | emd_4903_half_map_2.map | ||||||||||||
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Annotation | E1 control half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Echovirus E1
Entire | Name: Echovirus E1 |
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Components |
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-Supramolecule #1: Echovirus E1
Supramolecule | Name: 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 |
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Host (natural) | Organism: Homo sapiens (human) |
Virus shell | Shell ID: 1 / Name: icosahedral / Diameter: 300.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: VP1
Macromolecule | Name: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: E-1 (virus) / Strain: Human/Egypt/Farouk/1951 |
Molecular weight | Theoretical: 31.604373 KDa |
Sequence | String: 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 |
-Macromolecule #2: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: E-1 (virus) |
Molecular weight | Theoretical: 28.87226 KDa |
Sequence | String: 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 |
-Macromolecule #3: VP3
Macromolecule | Name: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: E-1 (virus) |
Molecular weight | Theoretical: 26.471074 KDa |
Sequence | String: 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 |
-Macromolecule #4: VP4
Macromolecule | Name: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Echovirus E1 |
Molecular weight | Theoretical: 7.398131 KDa |
Sequence | String: GAQVSTQKTG AHETSLSATG NSIIHYTNIN YYKDAASNSA NRQDFTQDPG KFTEPMKDVM IKTLPALN |
-Macromolecule #5: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ChemComp-PLM: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 / Details: 2 mM magnesium chloride in PBS |
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Grid | Model: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film 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 |
-Image processing
Particle selection | Number selected: 45309 |
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CTF correction | Software - Name: Gctf |
Startup model | Type of model: INSILICO MODEL / In silico model: Used Relion initial model protocol |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
Final 3D classification | Software - Name: RELION (ver. 2.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
Final reconstruction | Applied 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 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Protocol: RIGID BODY FIT |
Output model | PDB-6rjf: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-6rjf: |