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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 / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking ...lysis of host organelle involved in viral entry into host cell / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / nucleoside-triphosphate phosphatase / RNA-directed RNA polymerase / induction by virus of host autophagy / suppression by virus of host gene expression / ion channel activity / protein complex oligomerization / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / DNA replication / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding
P-loop containing nucleoside triphosphate hydrolase / 3C cysteine protease (picornain 3C) / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / Poliovirus core protein 3a, soluble domain / RNA-directed RNA polymerase, C-terminal domain / Viral coat protein subunit / Picornavirus coat protein VP4 superfamily / Picornavirus capsid / Picornavirus 2B protein ...P-loop containing nucleoside triphosphate hydrolase / 3C cysteine protease (picornain 3C) / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / Poliovirus core protein 3a, soluble domain / RNA-directed RNA polymerase, C-terminal domain / Viral coat protein subunit / Picornavirus coat protein VP4 superfamily / Picornavirus capsid / Picornavirus 2B protein / Picornavirus coat protein VP4 / AAA+ ATPase domain / picornavirus capsid protein / RNA-directed RNA polymerase, catalytic domain / Picornavirus/Calicivirus coat protein / RNA dependent RNA polymerase / RNA helicase / Picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus coat protein (VP4) / Poliovirus 3A protein like / RdRp of positive ssRNA viruses catalytic domain profile. / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Peptidase S1, PA clan / Picornavirales 3C/3C-like protease domain profile. / Helicase, superfamily 3, single-stranded RNA virus / Poliovirus 3A protein-like / Peptidase C3, picornavirus core protein 2A
Genome polyprotein
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.
Validation Report
SummaryFull reportAbout validation report
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
Remark 999AUTHORS STATE THAT RESIDUE 170 (CHAIN B) CAN BE ILE OR LEU, AS SEEN IN OTHER DATABASE REFERENCE SEQUENCES.
Remark 285THE ENTRY PRESENTED HERE DOES NOT CONTAIN THE COMPLETE CRYSTAL ASYMMETRIC UNIT. IN ADDITION, THE ...THE ENTRY PRESENTED HERE DOES NOT CONTAIN THE COMPLETE CRYSTAL ASYMMETRIC UNIT. IN ADDITION, THE COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME. IN ORDER TO GENERATE THE FULL CRYSTAL AU, APPLY THE FOLLOWING TRANSFORMATION MATRIX OR MATRICES AND SELECTED BIOMT RECORDS TO THE COORDINATES, AS SHOWN BELOW. X0 1 0.996500 -0.057200 0.060700 67.12416 X0 2 0.060700 0.996500 -0.057200 67.12416 X0 3 -0.057200 0.060700 0.996500 67.12416 CRYSTAL AU = (X0) * (BIOMT 1-5,11-15,21-25,36-40) * CHAINS A,B,C,D

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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)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
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
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
point symmetry operation5
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
point symmetry operation6
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
transform to crystal frame1
point symmetry operation20
Unit cell
γ
α
β
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))

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Components

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

#1: Protein/peptide 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/peptide 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/peptide 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/peptide 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 / Water

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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

Crystal-ID: 1

IDConc.Common nameSol-IDChemical formula
10.25 MHEPESreservoir
20.25 MreservoirNaCl
30.1 MreservoirCaCl2
40.3 %PEG8000reservoir
520000 mg/mlproteindrop

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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
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0078
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.54

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