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- PDB-1ncq: The structure of HRV14 when complexed with pleconaril, an antivir... -

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Basic information

Entry
Database: PDB / ID: 1ncq
TitleThe structure of HRV14 when complexed with pleconaril, an antiviral compound
Components(COAT PROTEIN ...) x 4
KeywordsVIRUS / rhinovirus 14 / HRV / pleconaril / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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-W11 / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus 14
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, Y. / Simpson, A.A. / Bator, C.M. / Chakravarty, S. / Pevear, D.C. / Skochko, G.A. / Tull, T.M. / Diana, G. / Rossmann, M.G.
CitationJournal: J.Virol. / Year: 2004
Title: Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds
Authors: Zhang, Y. / Simpson, A.A. / Ledford, R.M. / Bator, C.M. / Chakravarty, S. / Skochko, G.A. / Demenczuk, T.M. / Watanyar, A. / Pevear, D.C. / Rossmann, M.G.
History
DepositionDec 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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_remark / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_ncs_oper / struct_sheet / 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[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_torsion.phi / _pdbx_validate_torsion.psi / _struct_sheet.number_strands / _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 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999AUTHORS STATE THAT RESIDUE 170 (CHAIN B) CAN BE ILE OR LEU, AS SEEN IN OTHER DATABASE REFERENCE SEQUENCES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COAT PROTEIN VP1
B: COAT PROTEIN VP2
C: COAT PROTEIN VP3
D: COAT PROTEIN VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8645
Polymers94,4834
Non-polymers3811
Water4,360242
1
A: COAT PROTEIN VP1
B: COAT PROTEIN VP2
C: COAT PROTEIN VP3
D: COAT PROTEIN VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,691,833300
Polymers5,668,952240
Non-polymers22,88160
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
A: COAT PROTEIN VP1
B: COAT PROTEIN VP2
C: COAT PROTEIN VP3
D: COAT PROTEIN VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 474 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)474,31925
Polymers472,41320
Non-polymers1,9075
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN VP1
B: COAT PROTEIN VP2
C: COAT PROTEIN VP3
D: COAT PROTEIN VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 569 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)569,18330
Polymers566,89524
Non-polymers2,2886
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
A: COAT PROTEIN VP1
B: COAT PROTEIN VP2
C: COAT PROTEIN VP3
D: COAT PROTEIN VP4
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 1.9 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)1,897,278100
Polymers1,889,65180
Non-polymers7,62720
Water1,44180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)438.720, 438.720, 438.720
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(0.53790572, -0.78425723, 0.30921462), (0.77093857, 0.30920739, -0.55682665), (0.34108386, 0.53788079, 0.77092087)0.14338, 0.07293, -0.09943
3generate(-0.20980346, -0.49803398, 0.84140365), (0.46314759, -0.80851129, -0.36305871), (0.86109269, 0.31348275, 0.40028077)0.13256, 0.26139, -0.08795
4generate(-0.20981887, 0.46311895, 0.86109992), (-0.49801628, -0.80850682, 0.31352309), (0.84139194, -0.36308365, 0.4002917)-0.0175, 0.30493, 0.01857
5generate(0.53788079, 0.77092087, 0.34108386), (-0.78425723, 0.30921462, 0.53790572), (0.30920739, -0.55682665, 0.77093857)-0.09943, 0.14338, 0.07293
6generate(-0.36539438, -0.89398504, 0.25937942), (-0.89398504, 0.25937942, -0.36539438), (0.25937942, -0.36539438, -0.89398504)0.306, 0.306, 0.306
7generate(-0.79728515, 0.1496516, 0.58477042), (-0.40554419, 0.58477766, -0.70255278), (-0.44709882, -0.79726021, -0.40552649)0.16262, 0.23307, 0.40543
8generate(-0.11403629, 0.9860868, 0.12094949), (-0.00694631, 0.1209789, -0.99263258), (-0.99345422, -0.11400318, -0.00694261)0.00107, 0.28743, 0.3235
9generate(0.7401255, 0.45939551, -0.4910986), (-0.24904012, -0.49106273, -0.83475335), (-0.62464217, 0.74013873, -0.24906277)0.04461, 0.39395, 0.17344
10generate(0.58477766, -0.70255278, -0.40554419), (-0.79726021, -0.40552649, -0.44709882), (0.1496516, 0.58477042, -0.79728515)0.23307, 0.40543, 0.16262
11generate(-0.49106273, -0.83475335, -0.24904012), (0.74013873, -0.24906277, -0.62464217), (0.45939551, -0.4910986, 0.7401255)0.39395, 0.17344, 0.04461
12generate(-0.99263258, -0.00694631, 0.1209789), (-0.00694261, -0.99345422, -0.11400318), (0.12094949, -0.11403629, 0.9860868)0.28743, 0.3235, 0.00107
13generate(-0.49803398, 0.84140365, -0.20980346), (-0.80851129, -0.36305871, 0.46314759), (0.31348275, 0.40028077, 0.86109269)0.13256, 0.26139, -0.08795
14generate(0.30921462, 0.53790572, -0.78425723), (-0.55682665, 0.77093857, 0.30920739), (0.77092087, 0.34108386, 0.53788079)0.14338, 0.07293, -0.09943
15generate(0.31352309, -0.49801628, -0.80850682), (0.4002917, 0.84139194, -0.36308365), (0.86109992, -0.20981887, 0.46311895)0.30493, 0.01857, -0.0175
16generate(-0.36308365, 0.4002917, 0.84139194), (0.46311895, 0.86109992, -0.20981887), (-0.80850682, 0.31352309, -0.49801628)0.01857, -0.0175, 0.30493
17generate(0.40028077, 0.86109269, 0.31348275), (0.84140365, -0.20980346, -0.49803398), (-0.36305871, 0.46314759, -0.80851129)-0.08795, 0.13256, 0.26139
18generate(0.9860868, 0.12094949, -0.11403629), (0.1209789, -0.99263258, -0.00694631), (-0.11400318, -0.00694261, -0.99345422)0.00107, 0.28743, 0.3235
19generate(0.58477042, -0.79728515, 0.1496516), (-0.70255278, -0.40554419, 0.58477766), (-0.40552649, -0.44709882, -0.79726021)0.16262, 0.23307, 0.40543
20generate(-0.24906277, -0.62464217, 0.74013873), (-0.4910986, 0.7401255, 0.45939551), (-0.83475335, -0.24904012, -0.49106273)0.17344, 0.04461, 0.39395

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Components

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COAT PROTEIN ... , 4 types, 4 molecules ABCD

#1: Protein COAT PROTEIN VP1


Mass: 32560.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: hela cells / Species: Human rhinovirus B / References: UniProt: P03303
#2: Protein COAT PROTEIN VP2


Mass: 28501.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: hela cells / Species: Human rhinovirus B / References: UniProt: P03303
#3: Protein COAT PROTEIN VP3


Mass: 26236.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: hela cells / Species: Human rhinovirus B / References: UniProt: P03303
#4: Protein COAT PROTEIN VP4


Mass: 7183.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: hela cells / Species: Human rhinovirus B / References: UniProt: P03303

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Non-polymers , 2 types, 243 molecules

#5: Chemical ChemComp-W11 / 3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE / WIN63843


Mass: 381.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18F3N3O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growDetails: The crystal was soaked in stabilization buffer containing 2ug/ml pleconaril before data collection
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.25 MHEPES1reservoir
20.25 M1reservoirNaCl
30.1 M1reservoirCaCl2
40.3 %PEG80001reservoir
520000 mg/mlprotein1drop

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 671838 / Observed criterion σ(I): 0
Reflection
*PLUS
Num. measured all: 1675367 / Rmerge(I) obs: 70.3 / Rmerge F obs: 0.077
Reflection shell
*PLUS
% possible obs: 26.3 % / Rmerge(I) obs: 0.456

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Processing

RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.217 6383 random
Rwork0.216 --
obs0.217 671838 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6268 0 27 242 6537
Refinement
*PLUS
Rfactor Rfree: 0.216 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0078
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.54

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