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- PDB-2who: CRYSTAL STRUCTURE OF HEPATITIS C VIRUS NS5B POLYMERASE FROM 1B GE... -

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Basic information

Entry
Database: PDB / ID: 2who
TitleCRYSTAL STRUCTURE OF HEPATITIS C VIRUS NS5B POLYMERASE FROM 1B GENOTYPE IN COMPLEX WITH A NON-NUCLEOSIDE INHIBITOR
ComponentsRNA-DIRECTED RNA POLYMERASE
KeywordsTRANSFERASE / RNA REPLICATION / ENVELOPE PROTEIN / HEPATITIS C VIRUS / ENDOPLASMIC RETICULUM / NON NUCLEOSIDE INHIBITOR / VIRAL PROTEIN / METAL-BINDING / TRANSMEMBRANE / POLYMERASE / ATP-BINDING / GENOTYPE 1B / RNA-BINDING / RNA-DEPENDENT RNA POLYMERASE / NNI / HCV / NS5B / MEMBRANE / HELICASE / HYDROLASE / NUCLEOTIDE-BINDING / ALLOSTERIC INHIBITOR / RNA-DIRECTED RNA POLYMERASE
Function / homology
Function and homology information


hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / 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 transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / 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 / viral nucleocapsid / monoatomic ion transmembrane transport / 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 / ribonucleoprotein complex / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / 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, 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 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 core protein, chain A superfamily / : / 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 / NS3 RNA helicase, C-terminal helical domain / 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 / 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-VGI / Genome polyprotein
Similarity search - Component
Biological speciesHEPATITIS C VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDi Marco, S.
CitationJournal: J. Med. Chem. / Year: 2009
Title: Identification and biological evaluation of a series of 1H-benzo[de]isoquinoline-1,3(2H)-diones as hepatitis C virus NS5B polymerase inhibitors.
Authors: Ontoria, J.M. / Rydberg, E.H. / Di Marco, S. / Tomei, L. / Attenni, B. / Malancona, S. / Martin Hernando, J.I. / Gennari, N. / Koch, U. / Narjes, F. / Rowley, M. / Summa, V. / Carroll, S.S. ...Authors: Ontoria, J.M. / Rydberg, E.H. / Di Marco, S. / Tomei, L. / Attenni, B. / Malancona, S. / Martin Hernando, J.I. / Gennari, N. / Koch, U. / Narjes, F. / Rowley, M. / Summa, V. / Carroll, S.S. / Olsen, D.B. / De Francesco, R. / Altamura, S. / Migliaccio, G. / Carfi, A.
History
DepositionMay 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)120,3258
Polymers119,2832
Non-polymers1,0426
Water9,350519
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A: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1634
Polymers59,6421
Non-polymers5213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1634
Polymers59,6421
Non-polymers5213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.210, 96.999, 193.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.00056, -0.00077), (0.00056, -1, -0.00291), (-0.00077, -0.00291, 1)
Vector: 33.66388, 2.89224, 0.03013)

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Components

#1: Protein RNA-DIRECTED RNA POLYMERASE / NS5B / P68


Mass: 59641.508 Da / Num. of mol.: 2 / Fragment: NS5B, RESIDUES 2420-2955
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HEPATITIS C VIRUS / Strain: ISOLATE BK / Description: GENBANK ACCESSION NUMBER AB016785 / Variant: GENOTYPE 1B / Plasmid: PT7.7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26663, RNA-directed RNA polymerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-VGI / 2-(3-bromophenyl)-6-[(2-hydroxyethyl)amino]-1h-benzo[de]isoquinoline-1,3(2h)-dione


Mass: 411.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H15BrN2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNS5B PROTEIN, GENOTYPE 1B AND STRAIN BK, LACKING THE C- TERMINAL 55 AMINO ACIDS. TOTAL AMINO ACIDS ...NS5B PROTEIN, GENOTYPE 1B AND STRAIN BK, LACKING THE C- TERMINAL 55 AMINO ACIDS. TOTAL AMINO ACIDS 535, UNIPROT REFERENCE P26663, 2420-2955

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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: 2.56 Å3/Da / Density % sol: 51.55 % / Description: NONE
Crystal growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 60884 / % possible obs: 74.3 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.5 / % possible all: 63

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CSJ

1csj


Resolution: 2→95.35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.023 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FINAL MODEL ENCOMPASS RESIDUES 1-531, RESIDUES 532-536 ARE NOT IN DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.26579 3281 5.1 %RANDOM
Rwork0.21055 ---
obs0.21336 60884 74.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.734 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.87 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 2→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8242 0 56 519 8817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0218476
X-RAY DIFFRACTIONr_bond_other_d0.0020.027690
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.96411508
X-RAY DIFFRACTIONr_angle_other_deg0.893317892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93251060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.21298
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029362
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021698
X-RAY DIFFRACTIONr_nbd_refined0.2220.22090
X-RAY DIFFRACTIONr_nbd_other0.2420.29231
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.25070
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2448
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1050.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7271.55304
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35528566
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it233172
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2594.52942
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 221 -
Rwork0.296 3809 -
obs--63.8 %

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