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- PDB-2giq: Hepatitis C virus RNA-dependent RNA polymerase NS5B with NNI-2 in... -

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Basic information

Entry
Database: PDB / ID: 2giq
TitleHepatitis C virus RNA-dependent RNA polymerase NS5B with NNI-2 inhibitor
ComponentsRNA-directed RNA polymerase
KeywordsTRANSFERASE / HCV / HEPATITIS / NS5B / RNA-DEPENDENT RNA POLYMERASE
Function / homology
Function and homology information


hepacivirin / host cell mitochondrial membrane / 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 / 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 / SH3 domain binding / nucleoside-triphosphate phosphatase ...hepacivirin / host cell mitochondrial membrane / 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 / 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 / SH3 domain binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / 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 NS2, C-terminal domain / 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, 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 NS2, C-terminal domain / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / 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 zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepatitis C virus, Non-structural protein NS2 / : / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus non-structural 5a protein membrane anchor / 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 / Hepacivirus/Pegivirus NS3 protease domain profile. / Hepatitis C virus NS3 protease / Reverse transcriptase/Diguanylate cyclase domain / DEAD box, Flavivirus / Flavivirus DEAD 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 / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / 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-NN2 / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHarris, S.F.
CitationJournal: J.Virol. / Year: 2006
Title: Selection and characterization of replicon variants dually resistant to thumb- and palm-binding nonnucleoside polymerase inhibitors of the hepatitis C virus.
Authors: Le Pogam, S. / Kang, H. / Harris, S.F. / Leveque, V. / Giannetti, A.M. / Ali, S. / Jiang, W.R. / Rajyaguru, S. / Tavares, G. / Oshiro, C. / Hendricks, T. / Klumpp, K. / Symons, J. / Browner, ...Authors: Le Pogam, S. / Kang, H. / Harris, S.F. / Leveque, V. / Giannetti, A.M. / Ali, S. / Jiang, W.R. / Rajyaguru, S. / Tavares, G. / Oshiro, C. / Hendricks, T. / Klumpp, K. / Symons, J. / Browner, M.F. / Cammack, N. / Najera, I.
History
DepositionMar 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase
B: RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,3544
Polymers126,4992
Non-polymers8552
Water9,332518
1
A: RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6772
Polymers63,2501
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6772
Polymers63,2501
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.872, 105.416, 126.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA-directed RNA polymerase / NS5B / p68


Mass: 63249.555 Da / Num. of mol.: 2 / Fragment: HCV NS5B
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus (isolate BK) / Genus: Hepacivirus / Species: Hepatitis C virus / Strain: Genotype 1B; Strain BK / Gene: NS5B / Production host: Escherichia coli (E. coli) / References: UniProt: P26663, RNA-directed RNA polymerase
#2: Chemical ChemComp-NN2 / 1-(2-CYCLOPROPYLETHYL)-3-(1,1-DIOXIDO-2H-1,2,4-BENZOTHIADIAZIN-3-YL)-6-FLUORO-4-HYDROXYQUINOLIN-2(1H)-ONE


Mass: 427.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H18FN3O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 50mM Na Citrate pH 4.9, 26% PEG 4000, 7.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 137797 / Num. obs: 128433 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.118 / Χ2: 0.942 / Net I/σ(I): 6.1
Reflection shellResolution: 1.65→1.71 Å / % possible obs: 63.9 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 1.09 / Num. unique all: 8599 / Num. unique obs: 8599 / Χ2: 0.597

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→50 Å / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.228 6497 RANDOM
Rwork0.204 --
all0.205 137797 -
obs-121853 -
Displacement parametersBiso mean: 23.1 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8680 0 60 518 9258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229060
X-RAY DIFFRACTIONr_bond_other_d0.0010.028244
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9712328
X-RAY DIFFRACTIONr_angle_other_deg0.815319178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31551142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86222.747364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.571151540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7691572
X-RAY DIFFRACTIONr_chiral_restr0.0650.21386
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210062
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021860
X-RAY DIFFRACTIONr_nbd_refined0.2120.21829
X-RAY DIFFRACTIONr_nbd_other0.1740.28187
X-RAY DIFFRACTIONr_nbtor_refined0.1760.24500
X-RAY DIFFRACTIONr_nbtor_other0.080.25202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2422
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1930.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8051.57326
X-RAY DIFFRACTIONr_mcbond_other0.1291.52270
X-RAY DIFFRACTIONr_mcangle_it0.90529156
X-RAY DIFFRACTIONr_scbond_it1.54434111
X-RAY DIFFRACTIONr_scangle_it2.2464.53166
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.697 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 309 -
Rwork0.276 5577 -
obs--58.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2906-0.13780.23210.1683-0.18580.89430.05620.0680.0408-0.0106-0.0545-0.02540.00410.1116-0.0017-0.03960.00920.00120.0020.013-0.040116.3421-1.957-27.179
20.46190.23980.18710.57940.32251.50370.1323-0.06-0.06280.0176-0.08820.01070.2506-0.257-0.04410.0106-0.0642-0.0450.02260.0265-0.0404-1.5572-18.1084-20.4049
30.573-0.060.47120.4748-0.40271.6557-0.0148-0.09560.00580.07860.05220.0034-0.0818-0.1838-0.0375-0.0305-0.0159-0.01120.01540.0016-0.062512.0823-6.36422.7471
40.40930.117-0.18510.2243-0.21170.59340.0456-0.06280.00680.0096-0.0551-0.04630.02250.06630.0095-0.047-0.00050.0082-0.00620.0118-0.0261-26.43371.94423.7886
50.5042-0.01850.20290.76930.00520.84230.03880.05740.13160.0517-0.03460.0771-0.0856-0.1033-0.0042-0.0390.03670.0402-0.01010.02780.0084-43.908418.6644-2.492
60.72720.1546-0.47740.3954-0.21181.3015-0.02350.16740.0522-0.07940.0301-0.00790.1082-0.1214-0.0066-0.03490.01680.01980.0250.027-0.0471-30.93676.8969-26.0879
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1877 - 193
2X-RAY DIFFRACTION1AA226 - 286232 - 292
3X-RAY DIFFRACTION2AA188 - 225194 - 231
4X-RAY DIFFRACTION2AA287 - 370293 - 376
5X-RAY DIFFRACTION3AA371 - 562377 - 568
6X-RAY DIFFRACTION4BB1 - 1877 - 193
7X-RAY DIFFRACTION4BB226 - 286232 - 292
8X-RAY DIFFRACTION5BB188 - 225194 - 231
9X-RAY DIFFRACTION5BB287 - 370293 - 376
10X-RAY DIFFRACTION6BB371 - 562377 - 568

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