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- PDB-2plv: STRUCTURAL FACTORS THAT CONTROL CONFORMATIONAL TRANSITIONS AND SE... -

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Entry
Database: PDB / ID: 2plv
TitleSTRUCTURAL FACTORS THAT CONTROL CONFORMATIONAL TRANSITIONS AND SEROTYPE SPECIFICITY IN TYPE 3 POLIOVIRUS
Components(HUMAN POLIOVIRUS TYPE 1 (SUBUNIT ...) x 4
KeywordsVIRUS / PICORNAVIRUS / Icosahedral virus
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / 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-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / 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-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / 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 / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / 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 / Rhinovirus 14, subunit 4 / 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) / 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 / Few Secondary Structures / Irregular / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / SPHINGOSINE / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / Resolution: 2.88 Å
AuthorsFilman, D.J. / Hogle, J.M.
Citation
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.
#1: Journal: Molecular Aspects of Picornavirus Infection and Detection
Year: 1989
Title: Structural Basis for Serotypic Differences and Thermostability in Poliovirus
Authors: Hogle, J.M. / Filman, D.J. / Syed, R. / Chow, M. / Minor, P.D.
#2: Journal: Concepts in Viral Pathogenesis III / Year: 1989
Title: Structural Determinants of Serotype Specificity and Host Range in Poliovirus
Authors: Hogle, J.M. / Syed, R. / Yeates, T.O. / Jacobson, D. / Critchlow, T. / Filman, D.J.
#3: Journal: J.Virol. / Year: 1988
Title: Three-Dimensional Structure of Poliovirus Serotype 1 Neutralizing Determinants
Authors: Page, G.S. / Mosser, A.G. / Hogle, J.M. / Filman, D.J. / Rueckert, R.R. / Chow, M.
#4: Journal: J.Biol.Chem. / Year: 1988
Title: Structural Domains of the Poliovirus Polyprotein are Major Determinants for Proteolytic Cleavage at Gln-Gly Pairs
Authors: Ypma-Wong, M.F. / Filman, D.J. / Hogle, J.M. / Semler, B.L.
#5: Journal: Embo J. / Year: 1988
Title: Engineering a Poliovirus Type 2 Antigenic Site on a Type 1 Capsid Results in a Chimaeric Virus which is Neurovirulent for Mice
Authors: Martin, A. / Wychowski, C. / Couderc, T. / Crainic, R. / Hogle, J. / Girard, M.
#6: Journal: Sci.Am. / Year: 1987
Title: The Structure of Poliovirus
Authors: Hogle, J.M. / Chow, M. / Filman, D.J.
#7: Journal: Nature / Year: 1987
Title: Myristylation of Picornavirus Capsid Protein Vp4 and its Structural Significance
Authors: Chow, M. / Newman, J.F.E. / Filman, D. / Hogle, J.M. / Rowlands, D.J. / Brown, F.
#8: Journal: Crystallography in Molecular Biology / Year: 1986
Title: The Structure of Poliovirus at 2.9 Angstroms Resolution. Crystallographic Methods and Biological Implications
Authors: Hogle, J.M. / Chow, M. / Filman, D.J.
#9: Journal: Science / Year: 1985
Title: Three-Dimensional Structure of Poliovirus at 2.9 Angstroms Resolution
Authors: Hogle, J.M. / Chow, M. / Filman, D.J.
History
DepositionOct 17, 1989Processing site: BNL
Revision 1.0Oct 17, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
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_remark / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_ref_seq_dif / struct_site
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][2] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx_vector[3] / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Remark 700SHEET STRANDS 2, 3, AND 4 ARE COMMON TO SHEETS *1B1* AND *1B2*. THE SECOND STRAND OF SHEET *1B3* IS ...SHEET STRANDS 2, 3, AND 4 ARE COMMON TO SHEETS *1B1* AND *1B2*. THE SECOND STRAND OF SHEET *1B3* IS THE SAME AS THE THIRD STRAND OF SHEETS *1B1* AND *1B2*. STRANDS 1, 2, AND 3 ARE COMMON TO SHEETS *2B1*, *2B2*, AND *2B3*. STRANDS 1 AND 2 ARE COMMON TO SHEETS *2C1*, *2C2*, AND *2C3*. THE LAST FOUR STRANDS ARE COMMON TO SHEETS *3B1* AND *3B2*. SEQUENCE NUMBERING IS UNCERTAIN IN THE THIRD STRAND OF SHEET * 4N*. THE FIFTH AND SIXTH STRANDS OF SHEET * 3C* ARE FROM A THREEFOLD-RELATED PROTOMER. BECAUSE OF LIMITATIONS IMPOSED BY THE PROTEIN DATA BANK FORMAT IT IS NOT POSSIBLE TO PRESENT THIS SHEET ON SHEET RECORDS. INSTEAD THIS SHEET IS SPECIFIED IN THIS REMARK. 3C 7 ILE 3 82 LEU 3 87 0 3C 7 GLY 3 188 VAL 3 199 -1 N GLY 3 188 O LEU 3 87 3C 7 ALA 3 126 ALA 3 135 -1 N ALA 3 135 O TYR 3 189 3C 7 THR 3 152 ILE 3 158 -1 N THR 3 152 O TYR 3 134 3C 7 ASN 2 20 THR 2 25 1 O ASN 2 20 N HIS 3 153 3C 7 LEU 2 14 LEU 2 18 -1 N LEU 2 18 O SER 2 21 3C 7 THR 1 36 SER 1 38 -1 N THR 1 36 O THR 2 17 SHEET * TT* CONSISTS OF FIVE STRANDS. ALL FIVE STRANDS OF SHEET * TT* ARE FROM FIVEFOLD-RELATED PROTOMERS. BECAUSE OF LIMITATIONS IMPOSED BY THE PROTEIN DATA BANK FORMAT IT IS NOT POSSIBLE TO PRESENT THIS SHEET ON SHEET RECORDS. INSTEAD THIS SHEET IS SPECIFIED IN THIS REMARK. TT 5 LEU 3 2 THR 3 7 0 TT 5 LEU 3 2 THR 3 7 1 N LEU 3 2 O PRO 3 3 TT 5 LEU 3 2 THR 3 7 1 N LEU 3 2 O PRO 3 3 TT 5 LEU 3 2 THR 3 7 1 N LEU 3 2 O PRO 3 3 TT 5 LEU 3 2 THR 3 7 1 N LEU 3 2 O PRO 3 3 SHEET * 4M* CONSISTS OF THREE STRANDS. STRAND 3 OF SHEET * 4M* IS FROM A FIVEFOLD-RELATED PROTOMER. BECAUSE OF LIMITATIONS IMPOSED BY THE PROTEIN DATA BANK FORMAT IT IS NOT POSSIBLE TO PRESENT THIS SHEET ON SHEET RECORDS. INSTEAD THIS SHEET IS SPECIFIED IN THIS REMARK. 4M 3 ALA 1 21 SER 1 23 0 4M 3 GLN 4 44 SER 4 47 -1 N SER 4 47 O ALA 1 21 4M 3 ASN 4 15 ASN 4 17 -1 N ASN 4 17 O GLN 4 44

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP1)
2: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP2)
3: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP3)
4: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP4)
1: SPHINGOSINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9216
Polymers97,3934
Non-polymers5282
Water8,629479
1
1: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP1)
2: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP2)
3: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP3)
4: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP4)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,875,239360
Polymers5,843,567240
Non-polymers31,672120
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: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP1)
2: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP2)
3: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP3)
4: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP4)
hetero molecules
x 5


  • icosahedral pentamer
  • 490 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)489,60330
Polymers486,96420
Non-polymers2,63910
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP1)
2: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP2)
3: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP3)
4: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP4)
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 588 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)587,52436
Polymers584,35724
Non-polymers3,16712
Water43224
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: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP1)
2: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP2)
3: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP3)
4: HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP4)
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.94 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,937,619180
Polymers2,921,783120
Non-polymers15,83660
Water2,162120
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)322.940, 358.040, 380.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: RESIDUE PRO 2 83 IS A CIS PROLINE. / 2: POSSIBLE ANION SITE. / 3: POSSIBLE CATION SITE. / 4: SEE REMARK 6.
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.30930465, -0.81642343, 0.48763205), (0.80161055, 0.49971234, 0.32819023), (-0.51161448, 0.28937827, 0.80901699)46.3008, 31.16175, -18.13389
3generate(-0.80826389, -0.51939032, 0.27738728), (0.48060969, -0.30977009, 0.82040318), (-0.34018087, 0.79641188, 0.5)26.338, 77.89751, -47.47514
4generate(-0.80826389, 0.48060968, -0.34018318), (-0.51939032, -0.3097701, 0.79641728), (0.2773854, 0.82039762, 0.5)-32.30049, 75.62004, -47.47514
5generate(0.30930465, 0.80161055, -0.51161795), (-0.81642344, 0.49971234, 0.28938023), (0.48762875, 0.32818801, 0.80901699)-48.57827, 27.47673, -18.13389
6generate(-0.99698759, -0.07756126), (-0.07756126, 0.99698759), (-1)-189.90056
7generate(-0.37054682, 0.77520571, -0.51161795), (0.77520571, 0.56152983, 0.28938023), (0.51161448, -0.28937827, -0.80901699)-48.57827, 27.47673, -171.76667
8generate(0.76855237, 0.54185186, -0.34018318), (0.54185186, -0.26855237, 0.79641728), (0.34018087, -0.79641188, -0.5)-32.30049, 75.62004, -142.42542
9generate(0.84611363, -0.45513573, 0.27738728), (-0.45513573, -0.34611363, 0.82040318), (-0.2773854, -0.82039762, -0.5)26.338, 77.89751, -142.42542
10generate(-0.24505007, -0.83795409, 0.48763205), (-0.83795409, 0.43603308, 0.32819023), (-0.48762875, -0.32818801, -0.80901699)46.3008, 31.16175, -171.76667
11generate(-0.03878063, -0.00150621, 0.99925), (0.9984938, 0.03878063, 0.03881), (-0.03880974, 0.99924323)94.87907, 3.68502, -94.95028
12generate(-0.52443319, 0.32006998, 0.78900523), (0.32006998, -0.7845838, 0.53102295), (0.78899988, 0.53101935, 0.30901699)74.91627, 50.42078, -65.60903
13generate(-0.30930465, 0.81642343, 0.48763205), (-0.80161055, -0.49971234, 0.32819023), (0.51161448, -0.28937827, 0.80901699)46.3008, 31.16175, -18.13389
14generate(0.30930465, 0.80161055, 0.51161795), (-0.81642344, 0.49971234, -0.28938023), (-0.48762875, -0.32818801, 0.80901699)48.57827, -27.47673, -18.13389
15generate(0.4764977, 0.29610223, 0.82781523), (0.29610223, 0.8325193, -0.46822705), (-0.82780962, 0.46822388, 0.30901699)78.60129, -44.45829, -65.60903
16generate(0.03878063, 0.00150621, 0.99925), (-0.9984938, -0.03878063, 0.03881), (0.03880974, -0.99924323)94.87907, 3.68502, -94.95028
17generate(-0.49802835, 0.25825249, 0.82781523), (-0.3597815, 0.80704534, -0.46822705), (-0.78899988, -0.53101935, -0.30901699)78.60129, -44.45829, -124.29153
18generate(-0.37054682, 0.77520571, 0.51161795), (0.77520571, 0.56152983, -0.28938023), (-0.51161448, 0.28937827, -0.80901699)48.57827, -27.47673, -171.76667
19generate(0.24505007, 0.83795409, 0.48763205), (0.83795409, -0.43603308, 0.32819023), (0.48762875, 0.32818801, -0.80901699)46.3008, 31.16175, -171.76667
20generate(0.49802835, 0.3597815, 0.78900523), (-0.25825249, -0.80704534, 0.53102295), (0.82780962, -0.46822388, -0.30901699)74.91627, 50.42078, -124.29153
21generate(-0.03878063, 0.9984938, -0.03881), (-0.00150621, 0.03878063, 0.99925), (0.99924323, 0.03880974)-3.68502, 94.87907, -94.95028
22generate(0.80826389, 0.51939032, 0.27738728), (-0.48060969, 0.30977009, 0.82040318), (0.34018087, -0.79641188, 0.5)26.338, 77.89751, -47.47514
23generate(0.52443319, -0.32006998, 0.78900523), (-0.32006998, 0.7845838, 0.53102295), (-0.78899988, -0.53101935, 0.30901699)74.91627, 50.42078, -65.60903
24generate(-0.49802835, -0.3597815, 0.78900523), (0.25825249, 0.80704534, 0.53102295), (-0.82780962, 0.46822388, -0.30901699)74.91627, 50.42078, -124.29153
25generate(-0.84611363, 0.45513573, 0.27738728), (0.45513573, 0.34611363, 0.82040318), (0.2773854, 0.82039762, -0.5)26.338, 77.89751, -142.42542
26generate(0.03878063, -0.9984938, -0.03881), (0.00150621, -0.03878063, 0.99925), (-0.99924323, -0.03880974)-3.68502, 94.87907, -94.95028
27generate(-0.76855237, -0.54185186, -0.34018318), (-0.54185186, 0.26855237, 0.79641728), (-0.34018087, 0.79641188, -0.5)-32.30049, 75.62004, -142.42542
28generate(-0.49802835, 0.25825249, -0.82781523), (-0.3597815, 0.80704534, 0.46822705), (0.78899988, 0.53101935, -0.30901699)-78.60129, 44.45829, -124.29153
29generate(0.4764977, 0.29610223, -0.82781523), (0.29610223, 0.8325193, 0.46822705), (0.82780962, -0.46822388, 0.30901699)-78.60129, 44.45829, -65.60903
30generate(0.80826389, -0.48060968, -0.34018318), (0.51939032, 0.3097701, 0.79641728), (-0.2773854, -0.82039762, 0.5)-32.30049, 75.62004, -47.47514

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Components

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HUMAN POLIOVIRUS TYPE 1 (SUBUNIT ... , 4 types, 4 molecules 1234

#1: Protein HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP1)


Mass: 33376.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#2: Protein HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP2)


Mass: 30075.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#3: Protein HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP3)


Mass: 26547.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#4: Protein HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP4)


Mass: 7393.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300

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Non-polymers , 3 types, 481 molecules 1

#5: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#6: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


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


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE 1 OF CHAIN 4 IS A MYRISTOYL GROUP (MYR), COVALENTLY LINKED TO THE AMINO TERMINAL GLYCINE OF ...RESIDUE 1 OF CHAIN 4 IS A MYRISTOYL GROUP (MYR), COVALENTLY LINKED TO THE AMINO TERMINAL GLYCINE OF VP4 VIA AN AMIDE BOND (SEE REFERENCE 8 ABOVE).

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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 ℃ / pH: 7 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMPIPES11
25 mM11MgCl2
31 mM11CaCl2
40.5 M11NaCl

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Data collection

Reflection
*PLUS
Highest resolution: 2.88 Å / Lowest resolution: 9999 Å / Num. obs: 712617 / % possible obs: 72.6 %

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Processing

SoftwareName: REAL-SPACE / Version: REFINEMENT / Classification: refinement
RefinementHighest resolution: 2.88 Å
Details: RESIDUE 0 IS IDENTIFIED AS A SPHINGOSINE MOLECULE (SPH). THE PROVISIONAL IDENTIFICATION OF ELECTRON DENSITY AS SPHINGOSINE IS NOT BASED ON DIRECT CHEMICAL EVIDENCE (SEE REFERENCE 1 ABOVE).
RfactorNum. reflection% reflection
Rwork0.2 --
obs-712617 72.6 %
Refinement stepCycle: LAST / Highest resolution: 2.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6647 0 36 479 7162
Refinement
*PLUS
Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS

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