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- PDB-8wu2: Crystal structure of RNA-dependent RNA polymerases from Jingmen t... -

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Basic information

Entry
Database: PDB / ID: 8wu2
TitleCrystal structure of RNA-dependent RNA polymerases from Jingmen tick virus
ComponentsRNA polymerase
KeywordsVIRAL PROTEIN / RNA polymerases
Function / homology
Function and homology information


methyltransferase activity / methylation / viral RNA genome replication / RNA-dependent RNA polymerase activity / host cell nucleus / ATP binding / membrane
Similarity search - Function
RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
SELENIUM ATOM / NS5-like protein
Similarity search - Component
Biological speciesAmblyomma virus GXTV108v
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsLiu, Z. / Han, P. / Peng, Q. / Qi, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81871658 China
CitationJournal: HLIFE / Year: 2024
Title: Crystal structures of RNA-dependent RNA polymerases from Jingmen tick virus and Alongshan virus
Authors: Liu, Z. / Peng, Q. / Han, P. / Kuai, L. / Qi, J. / Shi, Y.
History
DepositionOct 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 2.0May 1, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / entity_src_gen / pdbx_nonpoly_scheme / pdbx_struct_mod_residue / struct_ref / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.country / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_nonpoly_scheme.auth_seq_num / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase
B: RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,6313
Polymers144,5522
Non-polymers791
Water10,953608
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.573, 61.446, 125.595
Angle α, β, γ (deg.)90.000, 104.640, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein RNA polymerase


Mass: 72275.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amblyomma virus GXTV108v / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P2RZ45
#2: Chemical ChemComp-SE / SELENIUM ATOM


Mass: 78.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Se
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.6→44.12 Å / Num. obs: 73966 / % possible obs: 90.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.77 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 14.1
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 1.09 / Num. unique obs: 3241

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
OASISphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→41.78 Å / SU ML: 0.3267 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 32.0993
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2776 1933 2.8 %
Rwork0.2303 67082 -
obs0.2316 69015 86.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.22 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8911 0 1 608 9520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00299111
X-RAY DIFFRACTIONf_angle_d0.575212316
X-RAY DIFFRACTIONf_chiral_restr0.04031322
X-RAY DIFFRACTIONf_plane_restr0.00481577
X-RAY DIFFRACTIONf_dihedral_angle_d5.23941239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.35191110.2643905X-RAY DIFFRACTION70.28
2.67-2.740.31271170.25474122X-RAY DIFFRACTION74.93
2.74-2.820.30631270.25054426X-RAY DIFFRACTION79.71
2.82-2.910.33361200.23834464X-RAY DIFFRACTION80.08
2.91-3.010.32411370.24374559X-RAY DIFFRACTION83.45
3.01-3.130.27121390.24714689X-RAY DIFFRACTION84.51
3.13-3.280.27441380.23764782X-RAY DIFFRACTION86.73
3.28-3.450.34121430.23484958X-RAY DIFFRACTION88.87
3.45-3.660.24291350.22274987X-RAY DIFFRACTION90.9
3.66-3.950.26381440.22225112X-RAY DIFFRACTION92.47
3.95-4.340.25221600.2065246X-RAY DIFFRACTION93.89
4.34-4.970.24091480.20735312X-RAY DIFFRACTION96.52
4.97-6.260.30011590.23235243X-RAY DIFFRACTION95.02
6.26-41.780.23831550.23775277X-RAY DIFFRACTION95.37

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