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- PDB-3cso: HCV Polymerase in complex with a 1,5 Benzodiazepine inhibitor -

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Basic information

Entry
Database: PDB / ID: 3cso
TitleHCV Polymerase in complex with a 1,5 Benzodiazepine inhibitor
ComponentsRNA-directed RNA polymerase
KeywordsTRANSFERASE / 1 / 5-Benzodiazepines / Hepatitis C Virus / NS5B / 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 / molecular adaptor activity / 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 / 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 / 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
Similarity search - Domain/homology
Chem-XNI / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus isolate
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.71 Å
AuthorsNyanguile, O.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2008
Title: 1,5-benzodiazepines, a novel class of hepatitis C virus polymerase nonnucleoside inhibitors.
Authors: Nyanguile, O. / Pauwels, F. / Van den Broeck, W. / Boutton, C.W. / Quirynen, L. / Ivens, T. / van der Helm, L. / Vandercruyssen, G. / Mostmans, W. / Delouvroy, F. / Dehertogh, P. / Cummings, ...Authors: Nyanguile, O. / Pauwels, F. / Van den Broeck, W. / Boutton, C.W. / Quirynen, L. / Ivens, T. / van der Helm, L. / Vandercruyssen, G. / Mostmans, W. / Delouvroy, F. / Dehertogh, P. / Cummings, M.D. / Bonfanti, J.F. / Simmen, K.A. / Raboisson, P.
History
DepositionApr 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 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)130,6374
Polymers129,6352
Non-polymers1,0022
Water3,999222
1
A: RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3182
Polymers64,8171
Non-polymers5011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3182
Polymers64,8171
Non-polymers5011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.962, 108.224, 133.304
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 / HCV-J4 Polymerase


Mass: 64817.262 Da / Num. of mol.: 2 / Fragment: UNP residues 2420-2989
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus isolate / Strain: HC-J4 / Gene: HCV-NS5B / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: O92972, RNA-directed RNA polymerase
#2: Chemical ChemComp-XNI / (11S)-10-acetyl-11-[4-(benzyloxy)-3-chlorophenyl]-3,3-dimethyl-2,3,4,5,10,11-hexahydro-1H-dibenzo[b,e][1,4]diazepin-1-one


Mass: 501.016 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H29ClN2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.75
Details: 5-8% PEG 6000, 100 mM Mg-salts, pH 6.75, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9763 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
20.9761
ReflectionResolution: 2.71→83.05 Å / Num. all: 42311 / Num. obs: 42311 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.162
Reflection shellResolution: 2.71→2.8 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.614 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
Mol.Rep.phasing
RefinementResolution: 2.71→83.05 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.892 / SU B: 22.48 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.759 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23943 2114 5 %RANDOM
Rwork0.18035 ---
all0.18331 42277 --
obs0.18331 40163 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.248 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2--0.29 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.71→83.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8730 0 72 222 9024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229046
X-RAY DIFFRACTIONr_bond_other_d0.0010.028266
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.97512287
X-RAY DIFFRACTIONr_angle_other_deg0.816319197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21951126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93422.575369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33151534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6671579
X-RAY DIFFRACTIONr_chiral_restr0.0980.21380
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029999
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021872
X-RAY DIFFRACTIONr_nbd_refined0.2110.22130
X-RAY DIFFRACTIONr_nbd_other0.1830.28465
X-RAY DIFFRACTIONr_nbtor_refined0.1830.24505
X-RAY DIFFRACTIONr_nbtor_other0.0860.25339
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2330
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1810.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.28
X-RAY DIFFRACTIONr_mcbond_it1.98327226
X-RAY DIFFRACTIONr_mcbond_other0.33222260
X-RAY DIFFRACTIONr_mcangle_it2.54439089
X-RAY DIFFRACTIONr_scbond_it3.94143994
X-RAY DIFFRACTIONr_scangle_it5.78163197
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 154 -
Rwork0.246 2924 -
obs--99.97 %
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)
10.3855-0.05070.18741.66690.23580.64330.04840.0935-0.1957-0.0204-0.0203-0.18050.20320.0443-0.028-0.047-0.011-0.0133-0.0231-0.01920.001925.25957.91955.444
20.0993-0.09360.09960.6541-0.46581.0969-0.0105-0.0127-0.04160.0389-0.0267-0.06950.08780.09140.0373-0.0871-0.0175-0.0041-0.05970.0003-0.076925.656.88927.231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 5634 - 566
2X-RAY DIFFRACTION2BB1 - 5634 - 566

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