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- PDB-1nd3: The structure of HRV16, when complexed with pleconaril, an antivi... -

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Basic information

Entry
Database: PDB / ID: 1nd3
TitleThe structure of HRV16, when complexed with pleconaril, an antiviral compound
Components(coat protein ...) x 4
KeywordsVIRUS / HRV16 / rhinovirus / piconaviridae / pleconaril / 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 / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis 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 / 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 / DNA replication / 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
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. / 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
Chem-W11 / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus 16
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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 6, 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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999AUTHORS STATE THAT RESIDUE 24 (CHAIN D) CAN BE ILE OR LEU, AS SEEN IN OTHER DATABASE REFERENCE SEQUENCES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)95,6276
Polymers95,1804
Non-polymers4472
Water8,395466
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)5,737,616360
Polymers5,710,811240
Non-polymers26,805120
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
  • 478 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)478,13530
Polymers475,90120
Non-polymers2,23410
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
  • 574 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)573,76236
Polymers571,08124
Non-polymers2,68112
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
Unit cell
Length a, b, c (Å)360.301, 343.331, 332.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

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Coat protein ... , 4 types, 4 molecules ABCD

#1: Protein coat protein VP1


Mass: 32501.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 16 / Genus: Rhinovirus / Cell line: Hela cells / Species: Human rhinovirus ARhinovirus / References: UniProt: Q82122
#2: Protein coat protein VP2


Mass: 28990.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 16 / Genus: Rhinovirus / Cell line: Hela cells / Species: Human rhinovirus ARhinovirus / References: UniProt: Q82122
#3: Protein coat protein VP3


Mass: 26314.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 16 / Genus: Rhinovirus / Cell line: Hela cells / Species: Human rhinovirus ARhinovirus / References: UniProt: Q82122
#4: Protein coat protein VP4


Mass: 7374.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 16 / Genus: Rhinovirus / Cell line: Hela cells / Species: Human rhinovirus ARhinovirus / References: UniProt: Q82122

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Non-polymers , 3 types, 468 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-W11 / 3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE / WIN63843 / Pleconaril


Mass: 381.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18F3N3O3 / Comment: antivirus*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

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: 2.8→20 Å / Num. obs: 731062 / Observed criterion σ(I): 3
Reflection
*PLUS
% possible obs: 95.1 % / Num. measured all: 1224998 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 62.6 % / Rmerge(I) obs: 0.191

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Processing

RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflectionSelection details
Rfree0.243 98098 random
Rwork0.247 --
obs0.247 731062 -
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6336 0 28 466 6830
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0065
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.34

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