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- PDB-1tmf: THREE-DIMENSIONAL STRUCTURE OF THEILER MURINE ENCEPHALOMYELITIS V... -

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Entry
Database: PDB / ID: 1tmf
TitleTHREE-DIMENSIONAL STRUCTURE OF THEILER MURINE ENCEPHALOMYELITIS VIRUS (BEAN STRAIN)
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 / COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


RNA-protein covalent cross-linking / : / host cell nucleolus / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity ...RNA-protein covalent cross-linking / : / host cell nucleolus / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / RNA helicase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
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 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid ...Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / 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 / 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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesTheiler's encephalomyelitis virus
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsLuo, M. / Toth, K.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Three-dimensional structure of Theiler murine encephalomyelitis virus (BeAn strain).
Authors: Luo, M. / He, C. / Toth, K.S. / Zhang, C.X. / Lipton, H.L.
History
DepositionFeb 20, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_ncs_oper / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[2] / _pdbx_database_status.process_site / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_angle.linker_flag / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ref_seq_dif.details
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation

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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)90,2654
Polymers90,2654
Non-polymers00
Water0
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)5,415,885240
Polymers5,415,885240
Non-polymers00
Water0
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
  • 451 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)451,32420
Polymers451,32420
Non-polymers00
Water0
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
  • 542 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)541,58924
Polymers541,58924
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
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
  • 2.71 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,707,943120
Polymers2,707,943120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation29
Unit cell
Length a, b, c (Å)331.860, 331.860, 796.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Atom site foot note1: PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO 2 85
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.88041924, -0.3956428, 0.26139761), (0.39564283, 0.30901699, -0.86485566), (0.26139761, 0.8648556, 0.42859775)66.96199, 116.94791, -146.3756
3generate(0.68693352, -0.2445207, 0.68434784), (0.24452072, -0.80901699, -0.53451019), (0.68434784, 0.53451015, -0.49595051)41.38479, 306.17359, -90.46509
4generate(0.68693352, 0.2445207, 0.68434784), (-0.24452072, -0.80901699, 0.53451019), (0.68434784, -0.53451015, -0.49595051)-41.38479, 306.17359, 90.46509
5generate(0.88041924, 0.3956428, 0.26139761), (-0.39564283, 0.30901699, 0.86485566), (0.26139761, -0.8648556, 0.42859775)-66.96199, 116.94791, 146.3756
6generate(-0.38429534, 0.92321021), (-1), (0.92321021, 0.38429534)338.4972
7generate(-0.09701607, 0.9504872, 0.29523194), (-0.39564283, -0.30901699, 0.86485566), (0.91326592, -0.0329015, 0.40603306)-160.86863, 221.54929, 5.56853
8generate(0.36781156, 0.5874334, -0.72085826), (-0.24452072, 0.80901699, 0.53451019), (0.89717573, -0.02033425, 0.44120544)-99.42228, 32.32361, 3.44154
9generate(0.36781156, -0.5874334, -0.72085826), (0.24452072, 0.80901699, -0.53451019), (0.89717573, 0.02033425, 0.44120544)99.42228, 32.32361, -3.44154
10generate(-0.09701607, -0.9504872, 0.29523194), (0.39564283, -0.30901699, -0.86485566), (0.91326592, 0.0329015, 0.40603306)160.86863, 221.54929, -5.56853
11generate(0.46160511, -0.8319541, -0.30785233), (-0.55484444, -0.83195416), (0.69214767, 0.5548444, -0.46160511)140.80707, 169.2486, -93.90664
12generate(-0.00322252, -0.7059665, 0.70823787), (-0.70596655, -0.5, -0.50160869), (0.70823787, -0.50160866, -0.49677748)119.48384, 253.8729, 84.89656
13generate(-0.09701607, 0.3956428, 0.91326592), (-0.95048727, -0.30901699, 0.0329015), (0.29523194, -0.8648556, 0.40603306)-66.96199, 221.54929, 146.3756
14generate(0.30984396, 0.9504872, 0.02389003), (-0.95048727, 0.30901699, 0.0329015), (0.02389003, -0.0329015, 0.99917303)-160.86863, 116.94791, 5.56853
15generate(0.65509083, 0.19179059, -0.73080256), (-0.70596655, 0.5, -0.50160869), (0.26919745, 0.84452135, 0.46294316)-32.46029, 84.6243, -142.93406
16generate(0.46160511, 0.8319541, -0.30785233), (0.55484444, 0.83195416), (0.69214767, -0.5548444, -0.46160511)-140.80707, 169.2486, 93.90664
17generate(0.65509083, -0.19179059, -0.73080256), (0.70596655, 0.5, 0.50160869), (0.26919745, -0.84452135, 0.46294316)32.46029, 84.6243, 142.93406
18generate(0.30984396, -0.9504872, 0.02389003), (0.95048727, 0.30901699, -0.0329015), (0.02389003, 0.0329015, 0.99917303)160.86863, 116.94791, -5.56853
19generate(-0.09701607, -0.3956428, 0.91326592), (0.95048727, -0.30901699, -0.0329015), (0.29523194, 0.8648556, 0.40603306)66.96199, 221.54929, -146.3756
20generate(-0.00322252, 0.7059665, 0.70823787), (0.70596655, -0.5, 0.50160869), (0.70823787, 0.50160866, -0.49677748)-119.48384, 253.8729, -84.89656
21generate(0.46160511, -0.5548444, 0.69214767), (-0.83195416, 0.55484444), (-0.30785233, -0.8319541, -0.46160511)93.90664, 169.2486, 140.80707
22generate(0.36781156, 0.2445207, 0.89717573), (-0.58743344, 0.80901699, 0.02033425), (-0.72085826, -0.53451015, 0.44120544)-41.38479, 32.32361, 90.46509
23generate(0.65509083, 0.7059665, 0.26919745), (-0.19179061, 0.5, -0.84452141), (-0.73080256, 0.50160866, 0.46294316)-119.48384, 84.6243, -84.89656
24generate(0.92643273, 0.19179059, -0.32394252), (-0.19179061, -0.5, -0.84452141), (-0.32394252, 0.84452135, -0.42643273)-32.46029, 253.8729, -142.93406
25generate(0.80685197, -0.5874334, -0.06254491), (-0.58743344, -0.80901699, 0.02033425), (-0.06254491, 0.02033425, -0.99783498)99.42228, 306.17359, -3.44154
26generate(0.46160511, 0.5548444, 0.69214767), (0.83195416, -0.55484444), (-0.30785233, 0.8319541, -0.46160511)-93.90664, 169.2486, -140.80707
27generate(0.80685197, 0.5874334, -0.06254491), (0.58743344, -0.80901699, -0.02033425), (-0.06254491, -0.02033425, -0.99783498)-99.42228, 306.17359, 3.44154
28generate(0.92643273, -0.19179059, -0.32394252), (0.19179061, -0.5, 0.84452141), (-0.32394252, -0.84452135, -0.42643273)32.46029, 253.8729, 142.93406
29generate(0.65509083, -0.7059665, 0.26919745), (0.19179061, 0.5, 0.84452141), (-0.73080256, -0.50160866, 0.46294316)119.48384, 84.6243, 84.89656
30generate(0.36781156, -0.2445207, 0.89717573), (0.58743344, 0.80901699, -0.02033425), (-0.72085826, 0.53451015, 0.44120544)41.38479, 32.32361, -90.46509

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Components

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


Mass: 30574.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Theiler's encephalomyelitis virus / Genus: Cardiovirus / Species: Theilovirus / Strain: BEAN / Organ: KIDNEY / References: UniProt: P08544
#2: Protein THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP2)


Mass: 29494.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Theiler's encephalomyelitis virus / Genus: Cardiovirus / Species: Theilovirus / Strain: BEAN / Organ: KIDNEY / References: UniProt: P08544
#3: Protein THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP3)


Mass: 25508.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Theiler's encephalomyelitis virus / Genus: Cardiovirus / Species: Theilovirus / Strain: BEAN / Organ: KIDNEY / References: UniProt: P08544
#4: Protein/peptide THEILER'S MURINE ENCEPHALOMYELITIS VIRUS (SUBUNIT VP4)


Mass: 4686.845 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Theiler's encephalomyelitis virus / Genus: Cardiovirus / Species: Theilovirus / Strain: BEAN / References: UniProt: P13899
Sequence detailsTHE SEQUENCE PRESENTED ON THE SEQRES RECORDS CORRESPONDS TO THE SEQUENCE IN THE COORDINATE RECORDS. ...THE SEQUENCE PRESENTED ON THE SEQRES RECORDS CORRESPONDS TO THE SEQUENCE IN THE COORDINATE RECORDS. NOTE THAT THERE ARE SIX SEQUENCE DIFFERENCES BETWEEN THIS ENTRY AND THE SEQUENCE GIVEN IN SWISSPROT ENTRY POLG_TMEVB: CHAIN RESIDUE ENTRY SWISSPROT 1 138 THR MET 1 139 ASP THR 1 140 THR ARG 3 192 GLN LYS 4 12 ASN GLN 4 13 GLU SER

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
20.02 Mboric acid1reservoir
1PEG33501reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 209592 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.131

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Processing

RefinementHighest resolution: 3.5 Å
Refinement stepCycle: LAST / Highest resolution: 3.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6260 0 0 0 6260
Refinement
*PLUS
Highest resolution: 3.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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