+Open data
-Basic information
Entry | Database: PDB / ID: 1ev1 | ||||||
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Title | ECHOVIRUS 1 | ||||||
Components | (ECHOVIRUS 1) x 4 | ||||||
Keywords | VIRUS / VIRAL COAT PROTEIN / CAPSID / PICORNAVIRUS / ECHOVIRUS / Icosahedral 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 / : / 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 / : / 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 / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Human echovirus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.55 Å | ||||||
Authors | Wien, M.W. / Filman, D.J. / Hogle, J.M. | ||||||
Citation | Journal: Acta Crystallogr D Biol Crystallogr / Year: 1998 Title: Structure determination of echovirus 1. Authors: D J Filman / M W Wien / J A Cunningham / J M Bergelson / J M Hogle / Abstract: The atomic structure of echovirus 1 (a member of the enterovirus genus of the picornavirus family) has been determined using cryo-crystallography and refined to 3.55 A resolution. Echovirus 1 ...The atomic structure of echovirus 1 (a member of the enterovirus genus of the picornavirus family) has been determined using cryo-crystallography and refined to 3.55 A resolution. Echovirus 1 crystallizes in space group P22121 with a = 352.45, b = 472.15 and c = 483.20 A. The crystals contain one full virus particle in the asymmetric unit allowing for 60-fold noncrystallographic symmetry averaging. The diffraction pattern shows strong pseudo-B-centering with reflections with h + l = 2n + 1 being systematically weak or absent below about 6 A resolution. The size of the unit cell and presence of pseudo-B-centering placed strong constraints on the allowed packing of the icosahedral particle in the crystal lattice. These constraints greatly facilitated the determination of the orientation and position of the virus by reducing the dimensionality of the search, but interactions between the crystallographic and noncrystallographic symmetries rendered the choice of space group ambiguous until very late in the structure determination. This structure determination provides a striking example of the power of packing analysis in molecular replacement and illustrates how subtle interactions between crystallographic and noncrystallographic symmetries can be resolved. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: A Pseudo-Cell Based Approach to Efficient Crystallographic Refinement of Viruses Authors: Jacobson, D.H. / Hogle, J.M. / Filman, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ev1.cif.gz | 152.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ev1.ent.gz | 122.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ev1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/1ev1 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/1ev1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) |
-Components
-Protein , 4 types, 4 molecules 1234
#1: Protein | Mass: 31604.373 Da / Num. of mol.: 1 / Fragment: VP1, VP2, VP3, VP4 / Source method: isolated from a natural source Details: ECHOVIRUS OBTAINED FROM THE ATCC, PASSED IN HELA CELLS, THEN PLAQUE PURIFIED AND EXPANDED Source: (natural) Human echovirus 1 / Genus: Enterovirus / Cell line: HELA CELLS / Species: Human enterovirus B / Strain: FAROUK STRAIN / References: UniProt: O91734 |
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#2: Protein | Mass: 28126.465 Da / Num. of mol.: 1 / Fragment: VP1, VP2, VP3, VP4 / Source method: isolated from a natural source Details: ECHOVIRUS OBTAINED FROM THE ATCC, PASSED IN HELA CELLS, THEN PLAQUE PURIFIED AND EXPANDED Source: (natural) Human echovirus 1 / Genus: Enterovirus / Cell line: HELA CELLS / Species: Human enterovirus B / Strain: FAROUK STRAIN / References: UniProt: O91734 |
#3: Protein | Mass: 26471.074 Da / Num. of mol.: 1 / Fragment: VP1, VP2, VP3, VP4 / Source method: isolated from a natural source Details: ECHOVIRUS OBTAINED FROM THE ATCC, PASSED IN HELA CELLS, THEN PLAQUE PURIFIED AND EXPANDED Source: (natural) Human echovirus 1 / Genus: Enterovirus / Cell line: HELA CELLS / Species: Human enterovirus B / Strain: FAROUK STRAIN / References: UniProt: O91734 |
#4: Protein | Mass: 7398.131 Da / Num. of mol.: 1 / Fragment: VP1, VP2, VP3, VP4 / Source method: isolated from a natural source Details: ECHOVIRUS OBTAINED FROM THE ATCC, PASSED IN HELA CELLS, THEN PLAQUE PURIFIED AND EXPANDED Source: (natural) Human echovirus 1 / Genus: Enterovirus / Cell line: HELA CELLS / Species: Human enterovirus B / Strain: FAROUK STRAIN / References: UniProt: O91734 |
-Non-polymers , 3 types, 16 molecules 1
#5: Chemical | #6: Chemical | ChemComp-MYR / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 30 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 6 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Aug 1, 1996 / Details: SUPPER LONG MIRRORS |
Radiation | Monochromator: SUPPER LONG MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.55→50 Å / Num. obs: 947283 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.136 |
Reflection shell | Resolution: 3.55→3.66 Å / Rmerge(I) obs: 0.241 |
Reflection | *PLUS Num. measured all: 3522138 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: N, CA, AND C ATOMS FROM POLIOVIRUS Resolution: 3.55→50 Å Isotropic thermal model: ISOTROPIC THERMAL MOTION THE MODEL WAS TAKEN INTO ACCOUNT BY USING 12 OR 16 RESOLUTION-DEPENDENT BIN SCALES IN ALL STRUCTURE FACTOR COMPARISONS. Details: PROTOMER-BOX-BASED PSEUDO-REAL-SPACE PROGRAM BY FILMAN, JACOBSON, AND HOGLE WAS ALSO USED.
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Refinement step | Cycle: LAST / Resolution: 3.55→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: STRICT ICOSAHEDRAL SYMMETRY WAS ENFORCED. TO GENERATE THE ASYMMETRIC UNIT IN P 21 21 2, THE ICOSAHEDRAL PARTICLE WAS ROTATED BY THE MATRIX: 0.52131 0.85335 -.00519 -.00061 0.00646 ...NCS model details: STRICT ICOSAHEDRAL SYMMETRY WAS ENFORCED. TO GENERATE THE ASYMMETRIC UNIT IN P 21 21 2, THE ICOSAHEDRAL PARTICLE WAS ROTATED BY THE MATRIX: 0.52131 0.85335 -.00519 -.00061 0.00646 0.99998 0.85337 -.52129 0.00389 AND TRANSLATED TO THE FRACTIONAL COORDINATES: 0.24950 0.19623 0.25000 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.55→3.66 Å / Total num. of bins used: 16
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Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.298 |