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- PDB-4e78: Crystal structure of a product state assembly of HCV NS5B genotyp... -

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Basic information

Entry
Database: PDB / ID: 4.0E+78
TitleCrystal structure of a product state assembly of HCV NS5B genotype 2a JFH-1 isolate with beta hairpin loop deletion bound to primer-template RNA with 3'-dG
Components
  • 5'-R(*U*AP*CP*CP*GP*(GDO))-3'
  • PROTEIN (RNA-directed RNA polymerase)
KeywordsVIRAL PROTEIN / TRANSFERASE/RNA / RDRP / loopless DELTA8 / ternary complex / product complex / Flaviviridae / hepatitis C virus / TRANSFERASE-RNA complex
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 / Dectin-2 family / 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 ...hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / Dectin-2 family / 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 / identical protein 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. / 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
RNA / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsEdwards, T.E. / Mosley, R.T.
CitationJournal: J.Virol. / Year: 2012
Title: Structure of hepatitis C virus polymerase in complex with primer-template RNA.
Authors: Mosley, R.T. / Edwards, T.E. / Murakami, E. / Lam, A.M. / Grice, R.L. / Du, J. / Sofia, M.J. / Furman, P.A. / Otto, M.J.
History
DepositionMar 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Jun 6, 2012Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: 5'-R(*U*AP*CP*CP*GP*(GDO))-3'
P: 5'-R(*U*AP*CP*CP*GP*(GDO))-3'
A: PROTEIN (RNA-directed RNA polymerase)


Theoretical massNumber of molelcules
Total (without water)67,4873
Polymers67,4873
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-17 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.270, 143.270, 92.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: RNA chain 5'-R(*U*AP*CP*CP*GP*(GDO))-3'


Mass: 1875.189 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (RNA-directed RNA polymerase) / NS5B / p68


Mass: 63736.203 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: E86Q, E87Q, Delta8 replaced with GG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Strain: JFH-1 / Gene: NS5B / Plasmid: VCID 5854 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99IB8, RNA-directed RNA polymerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsPROTEIN COMPRISES UNP RESIDUES 2443-3012 WITH RESIDUES 2886-2895 REPLACED WITH A GG LINKER.

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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: 4.05 Å3/Da / Density % sol: 69.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 4.37 mg/mL NS5B in 20 mM Tris, pH 8, 200 mM sodium chloride, 20% glycerol, 2 mM TCEP, 200 mM imidazole against 30% PEG3350, 0.1 M Bis-Tris propane, pH 6.0, 200 mM ammonium acetate soaked ...Details: 4.37 mg/mL NS5B in 20 mM Tris, pH 8, 200 mM sodium chloride, 20% glycerol, 2 mM TCEP, 200 mM imidazole against 30% PEG3350, 0.1 M Bis-Tris propane, pH 6.0, 200 mM ammonium acetate soaked overnight in precipitant supplemented with 15% ethylene glycol as cryoprotectant and 0.2 mM UACCG(3'DG), crystal tracking ID 227386E9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 16, 2011
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 24020 / Num. obs: 23671 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 59.642 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 22.04
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.9-2.980.8632.8110593173897.7
2.98-3.060.7333.2610261167797.6
3.06-3.150.5454.3510008163798.2
3.15-3.240.4095.69803161699.1
3.24-3.350.3126.989399155898.5
3.35-3.470.2429.048822147798.3
3.47-3.60.1811.858855147598.9
3.6-3.740.13415.178264138698.7
3.74-3.910.10319.298011134998.8
3.91-4.10.07923.887641130299.5
4.1-4.320.05930.367220123699.4
4.32-4.590.05333.026802116699
4.59-4.90.04836.386300108198.6
4.9-5.290.04538.566022102999.1
5.29-5.80.04735.91535592698.5
5.8-6.480.04537.88493785898.7
6.48-7.490.03249.5422075599.3
7.49-9.170.0275.18351763798.5
9.17-12.970.01594.21270950898.8
12.970.01482.79109326090.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E76

4e76


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.2018 / WRfactor Rwork: 0.164 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7916 / SU B: 14.346 / SU ML: 0.255 / SU R Cruickshank DPI: 0.7485 / SU Rfree: 0.3682 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.528 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1217 5.1 %RANDOM
Rwork0.198 ---
obs0.2 23671 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.53 Å2 / Biso mean: 55.1667 Å2 / Biso min: 24.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.75 Å21.37 Å20 Å2
2--2.75 Å20 Å2
3----4.12 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4051 201 0 37 4289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194369
X-RAY DIFFRACTIONr_bond_other_d0.0010.022858
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9366003
X-RAY DIFFRACTIONr_angle_other_deg1.0893.0016953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9185537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91822.5156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86715639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5581532
X-RAY DIFFRACTIONr_chiral_restr0.0780.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214756
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02903
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 91 -
Rwork0.364 1585 -
all-1676 -
obs--97.56 %

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