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- PDB-1tme: THREE-DIMENSIONAL STRUCTURE OF THEILER VIRUS -

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Basic information

Entry
Database: PDB / ID: 1tme
TitleTHREE-DIMENSIONAL STRUCTURE OF THEILER VIRUS
Components
  • THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP1)
  • THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP2)
  • THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP3)
  • THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP4)
KeywordsVIRUS / Icosahedral virus
Function / homology
Function and homology information


host cell nucleolus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / RNA helicase activity / RNA helicase / symbiont-mediated suppression of host gene expression ...host cell nucleolus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / RNA helicase activity / RNA helicase / 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 / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. ...Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirus coat protein / 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 / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesTheiler's encephalomyelitis virus
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsGrant, R.A. / Filman, D.J. / Hogle, J.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Three-dimensional structure of Theiler virus.
Authors: Grant, R.A. / Filman, D.J. / Fujinami, R.S. / Icenogle, J.P. / Hogle, J.M.
#1: Journal: Embo J. / Year: 1989
Title: Structural Factors that Control Conformational Transitions and Serotype Specificity in Type 3 Poliovirus
Authors: Filman, D.J. / Syed, R. / Chow, M. / Macadam, A.J. / Minor, P.D. / Hogle, J.M.
History
DepositionJan 30, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_oper_list / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Remark 285THE ENTRY PRESENTED HERE DOES NOT CONTAIN THE COMPLETE CRYSTAL ASYMMETRIC UNIT. IN ADDITION, THE ...THE ENTRY PRESENTED HERE DOES NOT CONTAIN THE COMPLETE CRYSTAL ASYMMETRIC UNIT. IN ADDITION, THE COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME. IN ORDER TO GENERATE THE FULL CRYSTAL AU, APPLY THE FOLLOWING TRANSFORMATION MATRIX OR MATRICES AND SELECTED BIOMT RECORDS TO THE COORDINATES, AS SHOWN BELOW. X0 1 1.000000 0.000000 0.000000 0.00000 X0 2 0.000000 1.000000 0.000000 0.00000 X0 3 0.000000 0.000000 1.000000 0.00000 CRYSTAL AU = (X0) * (BIOMT 1-5,11-15,21-30,41-50) * CHAINS 1,2,3,4

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP1)
2: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP2)
3: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP3)
4: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP4)


Theoretical massNumber of molelcules
Total (without water)92,8624
Polymers92,8624
Non-polymers00
Water5,891327
1
1: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP1)
2: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP2)
3: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP3)
4: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP4)
x 60


Theoretical massNumber of molelcules
Total (without water)5,571,700240
Polymers5,571,700240
Non-polymers00
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: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP1)
2: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP2)
3: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP3)
4: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP4)
x 5


  • icosahedral pentamer
  • 464 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)464,30820
Polymers464,30820
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP1)
2: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP2)
3: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP3)
4: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP4)
x 6


  • icosahedral 23 hexamer
  • 557 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)557,17024
Polymers557,17024
Non-polymers00
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
6
1: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP1)
2: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP2)
3: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP3)
4: THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP4)
x 30


  • crystal asymmetric unit, crystal frame
  • 2.79 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,785,850120
Polymers2,785,850120
Non-polymers00
Water2,162120
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)360.500, 338.400, 348.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO 1 105 / 2: CIS PROLINE - PRO 2 85
3: SOLVENT MOLECULES WITH OCCUPANCIES SIGNIFICANTLY GREATER THAN 1.0 ARE SUSPECTED TO BE ANION OR CATION SITES.
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

#1: Protein THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP1)


Mass: 30385.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Theiler's encephalomyelitis virus (STRAIN DA)
Genus: Cardiovirus / Species: Theilovirus / Strain: DA / Organ: BEAN / References: UniProt: P13899
#2: Protein THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP2)


Mass: 29544.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Theiler's encephalomyelitis virus (STRAIN DA)
Genus: Cardiovirus / Species: Theilovirus / Strain: DA / Organ: BEAN / References: UniProt: P13899
#3: Protein THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP3)


Mass: 25824.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Theiler's encephalomyelitis virus (STRAIN DA)
Genus: Cardiovirus / Species: Theilovirus / Strain: DA / Organ: BEAN / References: UniProt: P13899
#4: Protein THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP4)


Mass: 7107.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Theiler's encephalomyelitis virus (STRAIN DA)
Genus: Cardiovirus / Species: Theilovirus / Strain: DA / Organ: BEAN / References: UniProt: P13899
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSOLVENT MOLECULES WITH OCCUPANCIES SIGNIFICANTLY GREATER THAN 1.0 ARE SUSPECTED TO BE ANION OR CATION SITES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis / PH range low: 7.3 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlvirus1drop
310 mMNa PIPES1reservoir
21reservoirprogressively lower concentrationNaCl

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 473861 / Num. measured all: 1154291 / Rmerge(I) obs: 0.2

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Processing

SoftwareName: REAL-SPACE / Version: REFINEMENT / Classification: refinement
RefinementResolution: 2.8→30 Å
Details: THE ELECTRON DENSITY WAS INCONSISTENT WITH THE PREDICTED AMINO ACID SEQUENCE DERIVED FROM THE GENE SEQUENCE OF THE DA STRAIN OF TMEV AT THREE SITES. THE STRUCTURE PRESENTED IN THIS ENTRY ...Details: THE ELECTRON DENSITY WAS INCONSISTENT WITH THE PREDICTED AMINO ACID SEQUENCE DERIVED FROM THE GENE SEQUENCE OF THE DA STRAIN OF TMEV AT THREE SITES. THE STRUCTURE PRESENTED IN THIS ENTRY REFLECTS THE ELECTRON DENSITY AT THESE SITES. RESIDUE 214 OF VP1 WAS BUILT AS GLY. THIS RESIDUE HAS BEEN REPORTED TO BE EITHER LEU (Y.OHARA,S.STEIN,J.FU,L.STILLMAN, L.KLAMAN,R.P.ROOS (1988) VIROLOGY 164, 244-255) OR TRP (A.ZURBRIGGEN,J.M.HOGLE,R.S.FUJINAMI (1989) J.EXP.MED. 170, 2037-2049). SURROUNDING PORTIONS OF THE STRUCTURE PACK TOO CLOSELY TO PERMIT THIS RESIDUE TO HAVE A SIDE CHAIN AND NO SIDE CHAIN DENSITY IS VISIBLE IN THE MAP. RESIDUES 202 AND 230 OF VP3 ARE REPORTED TO BE ALA IN THE DATABASE BUT IN BOTH CASES THE ELECTRON DENSITY SUGGEST A LARGER SIDE CHAIN, EITHER THR OR VAL. A THR SIDE CHAIN WAS BUILT INTO POSITION 202 AND A VAL INTO POSITION 230. IN BOTH CASES THE CHANGE IN ASSIGNMENT IS CONSISTENT WITH THE LOCAL ENVIRONMENT OF THE SIDE CHAIN AND WITH THE SEQUENCE OF THE BEAN AND GDVII STRAINS OF TMEV. THE PRESENCE OF THR AT POSITION 202 HAS BEEN CONFIRMED BY THE SEQUENCING OF THE DA SEED STOCK (UNPUBLISHED DATA). ANOTHER DIFFERENCE BETWEEN THE SEQUENCE DATA BASE AND THE STRUCTURE PRESENTED IN THIS ENTRY IS AT RESIDUE 266 OF VP2 WHERE THE RESIDUE IN THE ENTRY WAS REFINED AS GLY INSTEAD OF ALA. THIS RESIDUE, THE CARBOXYL TERMINUS OF VP2, IS PARTLY DISORDERED AND NO SIDE CHAIN DENSITY WAS VISIBLE IN THE MAP.
RfactorNum. reflection% reflection
Rwork0.3 --
obs-473961 46 %
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5953 0 0 327 6280
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.04
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: 'PSEUDO-REAL SPACE PROCEDURE' / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. reflection obs: 473961 / Rfactor obs: 0.3
Solvent computation
*PLUS
Displacement parameters
*PLUS

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