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- PDB-2cjq: Bovine viral diarrhea virus CP7-R12 RNA-dependent RNA polymerase -

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Basic information

Entry
Database: PDB / ID: 2cjq
TitleBovine viral diarrhea virus CP7-R12 RNA-dependent RNA polymerase
ComponentsRNA-DIRECTED RNA POLYMERASERNA-dependent RNA polymerase
KeywordsTRANSFERASE / RNA-DEPENDENT RNA POLYMERASE / NUCLEOTIDYLTRANSFERASE / BOVINE VIRAL DIARRHEA VIRUS / BVDV / HELICASE / MEMBRANE / PROTEASE / HYDROLASE / RNA-DIRECTED RNA POLYMERASE / VIRAL POLYMERASE / NUCLEOTIDE-BINDING / TRANSMEMBRANE / THIOL PROTEASE / SERINE PROTEASE / ATP-BINDING / POLYPROTEIN / GLYCOPROTEIN
Function / homology
Function and homology information


pestivirus NS3 polyprotein peptidase / ribonuclease T2 / serine-type exopeptidase activity / ribonuclease T2 activity / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / clathrin-dependent endocytosis of virus by host cell ...pestivirus NS3 polyprotein peptidase / ribonuclease T2 / serine-type exopeptidase activity / ribonuclease T2 activity / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell endoplasmic reticulum membrane / viral protein processing / RNA helicase / induction by virus of host autophagy / 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 / virion attachment to host cell / GTP binding / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Pestivirus envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / Capsid protein C, pestivirus / Pestivirus nonstructural protein 2 / Pestivirus NS2, peptidase C74 / Capsid protein C, pestivirus / Pestivirus NS2 peptidase / Pestivirus nonstructural protein 2 (NS2) protease domain profile. / Pestivirus NS3, peptidase S31 / Pestivirus envelope glycoprotein E2 ...Pestivirus envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / Capsid protein C, pestivirus / Pestivirus nonstructural protein 2 / Pestivirus NS2, peptidase C74 / Capsid protein C, pestivirus / Pestivirus NS2 peptidase / Pestivirus nonstructural protein 2 (NS2) protease domain profile. / Pestivirus NS3, peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus envelope glycoprotein E2, domain D / Pestivirus NS3 polyprotein peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus NS3 protease (NS3pro) domain profile. / Peptidase C53, pestivirus Npro, interaction domain / Peptidase C53, pestivirus Npro / Pestivirus Npro endopeptidase C53 / Pestivirus N-terminal protease Npro domain profile. / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / : / Flavivirus NS3 helicase, C-terminal helical domain / Reverse transcriptase/Diguanylate cyclase domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal 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. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBOVINE VIRAL DIARRHEA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChoi, K.H. / Gallei, A. / Becher, P. / Rossmann, M.G.
CitationJournal: Structure / Year: 2006
Title: The Structure of Bovine Viral Diarrhea Virus RNA-Dependent RNA Polymerase and its Amino-Terminal Domain.
Authors: Choi, K.H. / Gallei, A. / Becher, P. / Rossmann, M.G.
History
DepositionApr 5, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-DIRECTED RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)82,3021
Polymers82,3021
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.244, 106.244, 55.387
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein RNA-DIRECTED RNA POLYMERASE / RNA-dependent RNA polymerase / BOVINE VIRAL DIARRHEA VIRUS CP7 POLYMERASE / NS5B


Mass: 82302.219 Da / Num. of mol.: 1 / Fragment: POLYMERASE DOMAIN, RESIDUES 3189-3907
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOVINE VIRAL DIARRHEA VIRUS / Strain: CP7 / Description: CP7-R12 GENERATED BY RNA RECOMBINATION / Plasmid: PCP7-R12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q96662, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsASN438 DUPLICATION DUE TO IN VITRO RNA RECOMBINATION

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 7.5
Details: 10% POLYETHYLENE GLYCOL 8000, 0.1M HEPES PH 7.5, 8% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9766
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 21373 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.3
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S48

1s48


Resolution: 2.6→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXISUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 2104 9.2 %RANDOM
Rwork0.2311 ---
obs0.2311 21373 93.8 %-
Solvent computationBsol: 44.7499 Å2 / ksol: 0.337098 e/Å3
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1--2.501 Å2-7.015 Å20 Å2
2---2.501 Å20 Å2
3---5.001 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4393 0 0 31 4424
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008111
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_deg1.43684
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.953
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER.PARAM

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