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- PDB-1ev1: ECHOVIRUS 1 -

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Basic information

Entry
Database: PDB / ID: 1ev1
TitleECHOVIRUS 1
Components(ECHOVIRUS 1) x 4
KeywordsVIRUS / 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 / channel activity ...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 / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / 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
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Picornavirus coat protein VP4 superfamily / Jelly Rolls - #20 / 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 coat protein VP4 / Rhinovirus 14, subunit 4 / Picornavirus coat protein VP4 superfamily / Jelly Rolls - #20 / 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 / Few Secondary Structures / Irregular / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / PALMITIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesHuman echovirus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsWien, 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
DepositionDec 2, 1997Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _refine.pdbx_starting_model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: ECHOVIRUS 1
2: ECHOVIRUS 1
3: ECHOVIRUS 1
4: ECHOVIRUS 1
1: PALMITIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0856
Polymers93,6004
Non-polymers4852
Water25214
1
1: ECHOVIRUS 1
2: ECHOVIRUS 1
3: ECHOVIRUS 1
4: ECHOVIRUS 1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,645,090360
Polymers5,616,003240
Non-polymers29,088120
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: ECHOVIRUS 1
2: ECHOVIRUS 1
3: ECHOVIRUS 1
4: ECHOVIRUS 1
hetero molecules
x 5


  • icosahedral pentamer
  • 470 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)470,42430
Polymers468,00020
Non-polymers2,42410
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: ECHOVIRUS 1
2: ECHOVIRUS 1
3: ECHOVIRUS 1
4: ECHOVIRUS 1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 565 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)564,50936
Polymers561,60024
Non-polymers2,90912
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)472.150, 483.200, 352.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

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Protein , 4 types, 4 molecules 1234

#1: Protein ECHOVIRUS 1


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
#2: Protein ECHOVIRUS 1


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 ECHOVIRUS 1


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 ECHOVIRUS 1


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

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Non-polymers , 3 types, 16 molecules 1

#5: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#6: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 30 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 277 K / pH: 6 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlvirus11
230 %sucrose11
31 mM11NaCl
410 mMPIPES11
525 mM11MgCl2
61 mM11CaCl2
710 mMPIPES1reservoir
825 mM1reservoirCaCl2
925 mM1reservoirMgCl2
102.5 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Aug 1, 1996 / Details: SUPPER LONG MIRRORS
RadiationMonochromator: SUPPER LONG MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 3.55→3.66 Å / Rmerge(I) obs: 0.241
Reflection
*PLUS
Num. measured all: 3522138

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / 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.
RfactorNum. reflection% reflection
Rwork0.263 --
obs0.263 947283 97.7 %
Refinement stepCycle: LAST / Resolution: 3.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6528 0 33 14 6575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.76
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.29
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS 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 shellResolution: 3.55→3.66 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rwork0.298 54758 -
obs--81 %
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.29
LS refinement shell
*PLUS
Rfactor obs: 0.298

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