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- PDB-1vrh: HRV14/SDZ 880-061 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1vrh
TitleHRV14/SDZ 880-061 COMPLEX
Components(RHINOVIRUS 14) x 4
KeywordsVIRUS / RHINOVIRUS COAT PROTEIN / ANTIVIRAL AGENTS / POLYPROTEIN / COAT PROTEIN / CORE PROTEIN / RNA POLYMERASE / HYDROLASE / THIOL PROTEASE / MYRISTYLATION / Icosahedral virus
Function / homology
Function and homology information


lysis of host organelle involved in viral entry into 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 ...lysis of host organelle involved in viral entry into 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 / endocytosis involved in viral entry into host cell / 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
Chem-SD8 / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus 14
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsOren, D.A. / Zhang, A. / Arnold, E.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Synthesis and activity of piperazine-containing antirhinoviral agents and crystal structure of SDZ 880-061 bound to human rhinovirus 14.
Authors: Oren, D.A. / Zhang, A. / Nesvadba, H. / Rosenwirth, B. / Arnold, E.
#1: Journal: Antiviral Res. / Year: 1995
Title: Sdz 35-682, a New Picornavirus Capsid-Binding Agent with Potent Antiviral Activity
Authors: Rosenwirth, B. / Oren, D.A. / Arnold, E. / Kis, Z.L. / Eggers, H.J.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Structure Determination of Antiviral Compound Sch 38057 Complexed with Human Rhinovirus 14
Authors: Zhang, A. / Nanni, R.G. / Li, T. / Arnold, G.F. / Oren, D.A. / Jacobo-Molina, A. / Williams, R.L. / Kamer, G. / Rubenstein, D.A. / Li, Y.
#3: Journal: Semin.Virol. / Year: 1992
Title: Three-Dimensional Structure-Activity Relationships for Antiviral Agents that Interact with Picornavirus Capsids
Authors: Zhang, A. / Nanni, R.G. / Oren, D.A. / Rozhon, E.J. / Arnold, E.
#4: Journal: J.Mol.Biol. / Year: 1990
Title: Analysis of the Structure of a Common Cold Virus, Human Rhinovirus 14, Refined at a Resolution of 3.0 A
Authors: Arnold, E. / Rossmann, M.G.
#5: Journal: Acta Crystallogr.,Sect.A / Year: 1988
Title: The Use of Molecular-Replacement Phases for the Refinement of the Human Rhinovirus 14 Structure
Authors: Arnold, E. / Rossmann, M.G.
#6: Journal: Nature / Year: 1985
Title: Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.J. / Johnson, J.E. / Kamer, G. / Luo, M. / Mosser, A.G.
History
DepositionFeb 26, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Jan 18, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / citation_author / database_PDB_matrix / pdbx_struct_oper_list / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_ncs_oper
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_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[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_main_chain_plane.improper_torsion_angle / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Mar 15, 2023Group: Advisory / Category: pdbx_database_remark
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: RHINOVIRUS 14
2: RHINOVIRUS 14
3: RHINOVIRUS 14
4: RHINOVIRUS 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8715
Polymers94,4834
Non-polymers3891
Water00
1
1: RHINOVIRUS 14
2: RHINOVIRUS 14
3: RHINOVIRUS 14
4: RHINOVIRUS 14
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,692,262300
Polymers5,668,952240
Non-polymers23,31060
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: RHINOVIRUS 14
2: RHINOVIRUS 14
3: RHINOVIRUS 14
4: RHINOVIRUS 14
hetero molecules
x 5


  • icosahedral pentamer
  • 474 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)474,35525
Polymers472,41320
Non-polymers1,9435
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: RHINOVIRUS 14
2: RHINOVIRUS 14
3: RHINOVIRUS 14
4: RHINOVIRUS 14
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 569 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)569,22630
Polymers566,89524
Non-polymers2,3316
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: RHINOVIRUS 14
2: RHINOVIRUS 14
3: RHINOVIRUS 14
4: RHINOVIRUS 14
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 1.9 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)1,897,421100
Polymers1,889,65180
Non-polymers7,77020
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)445.100, 445.100, 445.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.46428249, -0.82990465, 0.30935523), (0.84439659, 0.30935523, -0.43737202), (0.26727602, 0.46428249, 0.84439659)0.18336, 0.04923, -0.09998
3generate(-0.40252706, -0.49841714, 0.7678235), (0.53635794, -0.80813188, -0.2434001), (0.74181712, 0.31385302, 0.5926246)0.1967, 0.26302, -0.11254
4generate(-0.40252706, 0.53635794, 0.74181712), (-0.49841714, -0.80813188, 0.31385302), (0.7678235, -0.2434001, 0.5926246)0.02159, 0.34591, -0.02032
5generate(0.46428249, 0.84439659, 0.26727602), (-0.82990465, 0.30935523, 0.46428249), (0.30935523, -0.43737202, 0.84439659)-0.09998, 0.18336, 0.04923
6generate(-0.6305654, -0.70150875, 0.33207415), (-0.70150875, 0.33207415, -0.6305654), (0.33207415, -0.6305654, -0.70150875)0.34718, 0.34718, 0.34718
7generate(-0.79635651, 0.46046981, 0.39215364), (-0.21383107, 0.39215364, -0.89470238), (-0.56576752, -0.79635651, -0.21383107)0.16382, 0.29795, 0.44716
8generate(0.12389799, 0.98541842, -0.11662042), (-0.00727745, -0.11662042, -0.99315013), (-0.99226854, 0.12389799, -0.00727745)0.00127, 0.3675, 0.32559
9generate(0.85843766, 0.14787594, -0.49113956), (-0.36729797, -0.49113956, -0.7898572), (-0.35801899, 0.85843766, -0.36729797)0.08416, 0.45972, 0.15048
10generate(0.39215364, -0.89470238, -0.21383107), (-0.79635651, -0.21383107, -0.56576752), (0.46046981, 0.39215364, -0.79635651)0.29795, 0.44716, 0.16382
11generate(-0.49113956, -0.7898572, -0.36729797), (0.85843766, -0.36729797, -0.35801899), (0.14787594, -0.49113956, 0.85843766)0.45972, 0.15048, 0.08416
12generate(-0.99315013, -0.00727745, -0.11662042), (-0.00727745, -0.99226854, 0.12389799), (-0.11662042, 0.12389799, 0.98541842)0.3675, 0.32559, 0.00127
13generate(-0.49841714, 0.7678235, -0.40252706), (-0.80813188, -0.2434001, 0.53635794), (0.31385302, 0.5926246, 0.74181712)0.1967, 0.26302, -0.11254
14generate(0.30935523, 0.46428249, -0.82990465), (-0.43737202, 0.84439659, 0.30935523), (0.84439659, 0.26727602, 0.46428249)0.18336, 0.04923, -0.09998
15generate(0.31385302, -0.49841714, -0.80813188), (0.5926246, 0.7678235, -0.2434001), (0.74181712, -0.40252706, 0.53635794)0.34591, -0.02032, 0.02159
16generate(-0.2434001, 0.5926246, 0.7678235), (0.53635794, 0.74181712, -0.40252706), (-0.80813188, 0.31385302, -0.49841714)-0.02032, 0.02159, 0.34591
17generate(0.5926246, 0.74181712, 0.31385302), (0.7678235, -0.40252706, -0.49841714), (-0.2434001, 0.53635794, -0.80813188)-0.11254, 0.1967, 0.26302
18generate(0.98541842, -0.11662042, 0.12389799), (-0.11662042, -0.99315013, -0.00727745), (0.12389799, -0.00727745, -0.99226854)0.00127, 0.3675, 0.32559
19generate(0.39215364, -0.79635651, 0.46046981), (-0.89470238, -0.21383107, 0.39215364), (-0.21383107, -0.56576752, -0.79635651)0.16382, 0.29795, 0.44716
20generate(-0.36729797, -0.35801899, 0.85843766), (-0.49113956, 0.85843766, 0.14787594), (-0.7898572, -0.36729797, -0.49113956)0.15048, 0.08416, 0.45972

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Components

#1: Protein RHINOVIRUS 14 / HRV14


Mass: 32560.549 Da / Num. of mol.: 1 / Mutation: I(2 170)L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Production host: Homo sapiens (human) / References: UniProt: P03303
#2: Protein RHINOVIRUS 14 / HRV14


Mass: 28501.361 Da / Num. of mol.: 1 / Mutation: I(2 170)L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Production host: Homo sapiens (human) / References: UniProt: P03303
#3: Protein RHINOVIRUS 14 / HRV14


Mass: 26236.754 Da / Num. of mol.: 1 / Mutation: I(2 170)L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Production host: Homo sapiens (human) / References: UniProt: P03303
#4: Protein RHINOVIRUS 14 / HRV14


Mass: 7183.863 Da / Num. of mol.: 1 / Mutation: I(2 170)L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Production host: Homo sapiens (human) / References: UniProt: P03303
#5: Chemical ChemComp-SD8 / 2-[4-(2H-1,4-BENZOTHIAZINE-3-YL)-PIPERAZINE-1-LY]-1,3-THIAZOLE-4-CARBOXYLIC ACID ETHYLESTER / SDZ 880-061


Mass: 388.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N4O2S2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growDetails: 5 MG/ML OF SDZ 880-061 IN 200 MICROLITER DROPS FOR 3 - 4 CRYSTALS
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlvirus1drop
25 mMTris-HCl1drop
30.125-0.375 %(w/v)PEG80001drop
410 mM1dropCaCl2
510 mMTris-HCl1reservoir
60.25-0.75 %(w/v)PEG80001reservoir
720 mM1reservoirCaCl2

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.54
DetectorDetector: FILM / Date: Jun 1, 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRmerge(I) obs: 0.119
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 30 Å / Num. obs: 147189 / % possible obs: 25.8 %
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.5 Å / % possible obs: 16 % / Num. unique obs: 35847 / Rmerge(I) obs: 0.195

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Processing

SoftwareName: PURDUE / Version: DATA PROCESSING PACKAGE / Classification: data reduction
RefinementHighest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6268 0 26 0 6294

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