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- PDB-1yvf: Hepatitis C virus NS5B RNA-dependent RNA polymerase complex with ... -

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Basic information

Entry
Database: PDB / ID: 1yvf
TitleHepatitis C virus NS5B RNA-dependent RNA polymerase complex with inhibitor PHA-00729145
ComponentsHCV NS5B POLYMERASE
KeywordsTRANSFERASE / NS5B / polymerase / HCV / fingers / palm / thumb
Function / homology
Function and homology information


host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / lipid droplet / : ...host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / lipid droplet / : / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / induction by virus of host autophagy / symbiont entry into host cell / ribonucleoprotein complex / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b ...Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / Reverse transcriptase/Diguanylate cyclase domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Alpha-Beta Plaits / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PH7 / PHOSPHATE ION / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPfefferkorn, J.A. / Greene, M.L. / Nugent, R.A. / Gross, R.J. / Mitchell, M.A. / Finzel, B.C. / Harris, M.S. / Wells, P.A. / Shelly, J.A. / Anstadt, R.A. ...Pfefferkorn, J.A. / Greene, M.L. / Nugent, R.A. / Gross, R.J. / Mitchell, M.A. / Finzel, B.C. / Harris, M.S. / Wells, P.A. / Shelly, J.A. / Anstadt, R.A. / Kilkuskie, R.E. / Kopta, L.A. / Schwende, F.J.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2005
Title: Inhibitors of HCV NS5B polymerase. Part 1: Evaluation of the southern region of (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid.
Authors: Pfefferkorn, J.A. / Greene, M.L. / Nugent, R.A. / Gross, R.J. / Mitchell, M.A. / Finzel, B.C. / Harris, M.S. / Wells, P.A. / Shelly, J.A. / Anstadt, R.A. / Kilkuskie, R.E. / Kopta, L.A. / Schwende, F.J.
#1: Journal: To be Published
Title: Inhibitors of HCV NS5B polymerase: Part 2: Evaluation of the northern region of (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid
Authors: Pfefferkorn, J.A. / Nugent, R.A. / Gross, R.J. / Greene, M.L. / Mitchell, M.A. / Reding, M.T. / Funk, L.A. / Anderson, R. / Wells, P.A. / Shelly, J.A.
History
DepositionFeb 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE A database reference sequence could not be found for this structure at the time of processing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HCV NS5B POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3198
Polymers64,3821
Non-polymers9377
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: HCV NS5B POLYMERASE
hetero molecules

A: HCV NS5B POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,63816
Polymers128,7642
Non-polymers1,87414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area6220 Å2
ΔGint-63 kcal/mol
Surface area45130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.879, 90.879, 188.516
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-701-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HCV NS5B POLYMERASE


Mass: 64382.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Genus: Hepacivirus / Production host: Escherichia coli (E. coli) / References: UniProt: O93077, RNA-directed RNA polymerase

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Non-polymers , 5 types, 235 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PH7 / (2Z)-2-(BENZOYLAMINO)-3-[4-(2-BROMOPHENOXY)PHENYL]-2-PROPENOIC ACID


Mass: 438.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H16BrNO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.76 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 31629 / % possible obs: 98.3 % / Rmerge(I) obs: 0.076 / Χ2: 2.22
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.590.38331600.838199.2
2.59-2.690.28631131.071199.7
2.69-2.820.21431571.426199.6
2.82-2.960.16931601.777199.5
2.96-3.150.13731732.882199.6
3.15-3.390.11531663.856199.4
3.39-3.730.0831883.222199.3
3.73-4.270.0631672.267198.1
4.27-5.380.05131652.25196.8
5.38-500.04231802.707192.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.501data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1521 4.8 %CCP4 uniqueify 5%
Rwork0.24 ---
all0.24 30205 --
obs0.24 30205 94.5 %-
Solvent computationBsol: 50.7021 Å2 / ksol: 0.345769 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.302 Å2-7.18 Å20 Å2
2---8.302 Å20 Å2
3---16.605 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 58 228 4676
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3421.5
X-RAY DIFFRACTIONc_mcangle_it2.2022
X-RAY DIFFRACTIONc_scbond_it2.0592
X-RAY DIFFRACTIONc_scangle_it2.9592.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2pha729145_2.prmpha729145_2.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5glycerol.prmglycerol.top

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