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- PDB-1gx5: Hepatitis C Virus RNA Polymerase in Complex with GTP and Manganese -

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Basic information

Entry
Database: PDB / ID: 1gx5
TitleHepatitis C Virus RNA Polymerase in Complex with GTP and Manganese
ComponentsRNA-DIRECTED RNA POLYMERASERNA-dependent RNA polymerase
KeywordsTRANSFERASE / POLYPROTEIN / GLYCOPROTEIN / RNA-DIRECTED RNA POLYMERASE / CORE PROTEIN / COAT PROTEIN / ENVELOPE PROTEIN / HELICASE / ATP BINDING / TRANSMEMBRANE / NONSTRUCTURAL PROTEIN
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 / : ...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 / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / 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 / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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 / 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
GUANOSINE-5'-TRIPHOSPHATE / : / Genome polyprotein
Similarity search - Component
Biological speciesHEPATITIS C VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBressanelli, S. / Rey, F.A.
CitationJournal: J.Virol. / Year: 2002
Title: A Structural Analysis of the Hepatitis C Virus RNA Polymerase in Complex with Ribonucleotides
Authors: Bressanelli, S. / Tomei, L. / Rey, F.A. / De Francesco, R.
History
DepositionMar 27, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4156
Polymers60,2041
Non-polymers1,2115
Water11,746652
1
A: RNA-DIRECTED RNA POLYMERASE
hetero molecules

A: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,83112
Polymers120,4092
Non-polymers2,42210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area5130 Å2
ΔGint-49.8 kcal/mol
Surface area43360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.076, 96.225, 95.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHE BIOLOGICAL OLIGOMERIZATION STATE OF THE PROTEIN IS NOT KNOWN.THE PARTICULAR CRYSTAL CONTACT OBSERVED IN THIS CRYSTAL IS NOTOBSERVED IN OTHER CRYSTAL FORMS OF THE PROTEIN

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Components

#1: Protein RNA-DIRECTED RNA POLYMERASE / RNA-dependent RNA polymerase


Mass: 60204.258 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 2420-2955
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HEPATITIS C VIRUS (ISOLATE BK) / Plasmid: PT7.7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P26663, RNA-directed RNA polymerase
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.6 Å3/Da / Density % sol: 51 %
Crystal growpH: 6.8
Details: 4% (W/V) PEG 4000, 0.1 M SODIUM CITRATE, 7% 2-PROPANOL, pH 6.80
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: Bressanelli, S., (1999) Proc. Natl. Acad. Sci. U.S.A., 96, 13034.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
220 mMHEPES1drop
320 mMdithiothreitol1drop
41 mMEDTA1drop
55 %(w/v)PEG80001reservoir
60.1 Msodium citrate1reservoir
75 %(v/v)2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 68538 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.3
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.9 / % possible all: 98.3
Reflection
*PLUS
Lowest resolution: 25 Å
Reflection shell
*PLUS
Lowest resolution: 1.73 Å / % possible obs: 98.5 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CSJ

1csj


Resolution: 1.7→24.78 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1717311.67 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3537 5.2 %RANDOM
Rwork0.193 ---
obs0.193 68538 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.9482 Å2 / ksol: 0.326738 e/Å3
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1-4.82 Å20 Å20 Å2
2---8.01 Å20 Å2
3---3.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4125 0 48 652 4825
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.91.5
X-RAY DIFFRACTIONc_mcangle_it3.822
X-RAY DIFFRACTIONc_scbond_it4.572
X-RAY DIFFRACTIONc_scangle_it6.072.5
LS refinement shellResolution: 1.7→1.74 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.319 207 4.6 %
Rwork0.285 4245 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GTP7_0.PARAMGTP7.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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