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- PDB-2hwe: A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 ... -

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Entry
Database: PDB / ID: 2hwe
TitleA COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A
Components
  • HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)
  • HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)
  • HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)
  • HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)
KeywordsVIRUS / RHINOVIRUS COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


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 / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase ...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 / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / 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 / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
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) ...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 / 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-W54 / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus 1A
MethodX-RAY DIFFRACTION / Resolution: 3.8 Å
AuthorsKim, K.H. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A.
Authors: Kim, K.H. / Willingmann, P. / Gong, Z.X. / Kremer, M.J. / Chapman, M.S. / Minor, I. / Oliveira, M.A. / Rossmann, M.G. / Andries, K. / Diana, G.D. / Dutko, F.J. / McKinlay, M.A. / Pevear, D.C.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Human Rhinovirus 14 Complexed with Antiviral Compound R 61837
Authors: Chapman, M.S. / Minor, I. / Rossmann, M.G. / Diana, G.D. / Andries, K.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of Human Rhinovirus Serotype 1A (Hrv1A)
Authors: Kim, S. / Smith, T.J. / Chapman, M.S. / Rossmann, M.G. / Pevear, D.C. / Dutko, F.J. / Felock, P.J. / Diana, G.D. / Mckinlay, M.A.
#3: Journal: Biochemistry / Year: 1988
Title: Structural Analysis of a Series of Antiviral Agents Complexed with Human Rhinovirus 14
Authors: Badger, J. / Minor, I. / Kremer, M.J. / Oliveira, M.A. / Smith, T.J. / Griffith, J.P. / Guerin, D.M.A. / Krishnaswamy, S. / Luo, M. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Dutko, F. ...Authors: Badger, J. / Minor, I. / Kremer, M.J. / Oliveira, M.A. / Smith, T.J. / Griffith, J.P. / Guerin, D.M.A. / Krishnaswamy, S. / Luo, M. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Dutko, F.J. / Fancher, M. / Rueckert, R.R. / Heinz, B.A.
#4: Journal: Science / Year: 1986
Title: The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating
Authors: Smith, T.J. / Kremer, M.J. / Luo, M. / Vriend, G. / Arnold, E. / Kamer, G. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Otto, M.J.
#5: 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. / Rueckert, R.R. / Sherry, B. / Vriend, G.
History
DepositionJan 25, 1994Processing site: BNL
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2012Group: Source and taxonomy
Revision 2.0Feb 8, 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_oper_list / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_ncs_oper / 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[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_database_status.process_site / _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_peptide_omega.omega / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _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
Revision 2.1Mar 15, 2023Group: Advisory / Category: pdbx_database_remark

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8705
Polymers92,4864
Non-polymers3831
Water0
1
1: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,572,172300
Polymers5,549,176240
Non-polymers22,99660
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: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 5


  • icosahedral pentamer
  • 464 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)464,34825
Polymers462,43120
Non-polymers1,9165
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 557 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)557,21730
Polymers554,91824
Non-polymers2,3006
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: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 10


  • crystal asymmetric unit, crystal frame
  • 929 kDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)928,69550
Polymers924,86340
Non-polymers3,83310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)341.300, 341.300, 465.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Atom site foot note1: LYS 1 98 - TRP 1 99 OMEGA = 216.55 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: PRO 1 150 - GLY 1 151 OMEGA = 251.74 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO 3 93 / 4: CIS PROLINE - PRO 3 235
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.56363135, -0.75576154, 0.33338397), (0.75581305, 0.30901668, -0.57728236), (0.33326614, 0.57735015, 0.74538593)110.09668, 6.33845, -84.09901
3generate(-0.14242854, -0.46703455, 0.87269318), (0.46717012, -0.80901718, -0.35671208), (0.87261991, 0.35688978, 0.33341172)139.323, 140.05852, -106.43423
4generate(-0.14242891, 0.46717008, 0.87262064), (-0.46703407, -0.80901679, 0.3568902), (0.87269274, -0.35671236, 0.33341172)47.28918, 216.36362, -36.13915
5generate(0.56363075, 0.7558133, 0.33326659), (-0.75576107, 0.30901731, 0.57735039), (0.33338398, -0.57728238, 0.74538593)-38.81717, 129.8027, 29.64083
6generate(0.16673337, 0.64541332, -0.74541405), (-0.64552899, -0.49999974, -0.57731465), (-0.74531312, 0.57744419, 0.33326637)165.42984, 325.18945, 147.95292
7generate(0.3333667, -0.35693209, -0.87262064), (-0.93414613, 4.502E-5, -0.3568902), (0.1274244, 0.93413027, -0.33341172)250.56614, 299.50122, 41.52915
8generate(-0.37269292, -0.86605136, -0.33324944), (-0.64541945, 0.49995502, -0.57747627), (0.6667334, -0.00013592, -0.74529608)358.39285, 226.66923, 89.51868
9generate(-0.97569509, -0.17835896, 0.12730688), (-0.1783594, 0.30887163, -0.93423039), (0.12730717, -0.93423027, -0.33317653)339.89712, 207.34481, 225.60162
10generate(-0.64231131, 0.75577758, -0.12742485), (-0.1784271, -0.30913439, -0.9341305), (-0.74538556, -0.57726613, 0.33341172)220.63943, 268.23366, 261.71597

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Components

#1: Protein HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)


Mass: 32610.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 1A / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P23008
#2: Protein HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)


Mass: 29114.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 1A / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P23008
#3: Protein HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)


Mass: 26176.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 1A / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P23008
#4: Protein/peptide HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)


Mass: 4583.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 1A / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P23008
#5: Chemical ChemComp-W54 / 5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLY)PHENOXY)PENTYL)-3-METHYL ISOXAZOLE / WIN54954


Mass: 383.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20Cl2N2O3
Nonpolymer detailsWIN54954 IS 5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL) PHENOXY)PENTYL)-3-METHYL ISOXAZOLE.

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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: 7.2 / Method: vapor diffusion, hanging drop
Details: referred to 'Arnold,E.', (1984) J. Mol. Biol., 177, 417-430
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlvirus1drop
20.125 %(w/v)PEG80001drop
30.01 M1dropCaCl2
40.01 MTris-HCl1drop
50.25 %(w/v)PEG80001reservoir
60.02 M1reservoirCaCl2
70.01 MTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.6 Å / Num. obs: 37153 / Redundancy: 1.35 % / Rmerge(I) obs: 0.119

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Processing

RefinementHighest resolution: 3.8 Å
Details: THIS STRUCTURE OF HUMAN RHINOVIRUS 1A COMPLEXED WITH A DRUG HAS NOT BEEN REFINED. RESIDUES CLOSE TO THE DRUG HAVE BEEN MODELED DIFFERENTLY THAN IN THE NATIVE STRUCTURE DUE TO VARIOUS ...Details: THIS STRUCTURE OF HUMAN RHINOVIRUS 1A COMPLEXED WITH A DRUG HAS NOT BEEN REFINED. RESIDUES CLOSE TO THE DRUG HAVE BEEN MODELED DIFFERENTLY THAN IN THE NATIVE STRUCTURE DUE TO VARIOUS CONFORMATIONAL CHANGES THAT OCCURRED UPON THE DRUG ENTRY. OTHER RESIDUES HAVE BEEN LEFT AT THE SAME POSITION AS IN THE NATIVE STRUCTURE.
Refinement stepCycle: LAST / Highest resolution: 3.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6223 0 25 0 6248

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