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- PDB-1s49: Crystal Structure of RNA-dependent RNA polymerase construct 1 (re... -

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Basic information

Entry
Database: PDB / ID: 1s49
TitleCrystal Structure of RNA-dependent RNA polymerase construct 1 (residues 71-679) from bovine viral diarrhea virus complexed with GTP
ComponentsRNA-dependent RNA polymerase
KeywordsREPLICATION / RNA BINDING PROTEIN / polymerase / RNA synthesis / de novo initiation / primer independent initiation / GTP binding / bovine viral diarrhea virus / BVDV
Function / homology
Function and homology information


pestivirus NS3 polyprotein peptidase / ribonuclease T2 / RNA stabilization / DNA/DNA annealing activity / serine-type exopeptidase activity / ribonuclease T2 activity / RNA strand annealing activity / viral genome packaging / host cell cytoplasmic vesicle / protein-DNA complex ...pestivirus NS3 polyprotein peptidase / ribonuclease T2 / RNA stabilization / DNA/DNA annealing activity / serine-type exopeptidase activity / ribonuclease T2 activity / RNA strand annealing activity / viral genome packaging / host cell cytoplasmic vesicle / protein-DNA complex / : / 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 / 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 / virion attachment to host cell / GTP binding / virion membrane / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / ATP binding / membrane / identical protein binding
Similarity search - Function
Cleavage inducing molecular chaperone, Jiv / Cleavage inducing molecular chaperone / 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. ...Cleavage inducing molecular chaperone, Jiv / Cleavage inducing molecular chaperone / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Alpha-Beta Plaits / 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 speciesBovine viral diarrhea virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å
AuthorsChoi, K.H. / Groarke, J.M. / Young, D.C. / Kuhn, R.J. / Smith, J.L. / Pevear, D.C. / Rossmann, M.G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation.
Authors: Choi, K.H. / Groarke, J.M. / Young, D.C. / Kuhn, R.J. / Smith, J.L. / Pevear, D.C. / Rossmann, M.G.
History
DepositionJan 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0142
Polymers70,4911
Non-polymers5231
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RNA-dependent RNA polymerase
hetero molecules

A: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,0284
Polymers140,9812
Non-polymers1,0462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_675-x+1,-y+2,z1
Buried area6830 Å2
ΔGint-29 kcal/mol
Surface area50560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)205.727, 205.727, 99.597
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
DetailsThe monomer asymmetric unit comprises the biological entity

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Components

#1: Protein RNA-dependent RNA polymerase /


Mass: 70490.742 Da / Num. of mol.: 1 / Fragment: Residues 71-679
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine viral diarrhea virus 1 / Genus: Pestivirus / Gene: NS5B / Production host: Escherichia coli (E. coli) / References: UniProt: P19711
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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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: 4.31 Å3/Da / Density % sol: 71.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium sulfate, isopropanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.928 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 25243 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rsym value: 0.07
Reflection shellResolution: 3→3.11 Å / Rsym value: 0.12 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3→29.78 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 208895.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2514 10.1 %RANDOM
Rwork0.264 ---
all0.2684 24972 --
obs0.264 24972 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.9965 Å2 / ksol: 0.338906 e/Å3
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å212.6 Å20 Å2
2--0.49 Å20 Å2
3---2.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4740 0 32 0 4772
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_mcbond_it6.271.5
X-RAY DIFFRACTIONc_mcangle_it9.722
X-RAY DIFFRACTIONc_scbond_it8.562
X-RAY DIFFRACTIONc_scangle_it12.462.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 426 10.5 %
Rwork0.362 3635 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GTP.PARAMGTP.TOP

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