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- PDB-5muy: Structure of a C-terminal domain of a reptarenavirus L protein wi... -

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Basic information

Entry
Database: PDB / ID: 5muy
TitleStructure of a C-terminal domain of a reptarenavirus L protein with m7GTP
ComponentsL protein
KeywordsVIRAL PROTEIN / arenavirus / polymerase / putative cap-binding
Function / homology
Function and homology information


cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / metal ion binding
Similarity search - Function
RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCAS virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsRosenthal, M. / Gogrefe, N. / Reguera, J. / Vogel, D. / Rauschenberger, B. / Cusack, S. / Gunther, S. / Reindl, S.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationRE 3712/1-1 Germany
German Research FoundationGU 883/1-1 Germany
German Research FoundationGU 883/4-1 Germany
CitationJournal: PLoS Pathog. / Year: 2017
Title: Structural insights into reptarenavirus cap-snatching machinery.
Authors: Rosenthal, M. / Gogrefe, N. / Vogel, D. / Reguera, J. / Rauschenberger, B. / Cusack, S. / Gunther, S. / Reindl, S.
History
DepositionJan 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 2.0Jan 17, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L protein
B: L protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0393
Polymers74,4992
Non-polymers5391
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-13 kcal/mol
Surface area30990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.340, 76.601, 116.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein L protein


Mass: 37249.723 Da / Num. of mol.: 2 / Fragment: C-terminus, UNP residues 1721-2046
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAS virus / Production host: Escherichia coli (E. coli) / References: UniProt: J7HBG8
#2: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 37% Jeffamine ED-2001, 2 mM TCEP and 100 mM HEPES pH 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.99→63.93 Å / Num. obs: 46169 / % possible obs: 97 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.1481 / Rrim(I) all: 0.2094 / Net I/σ(I): 4.24
Reflection shellResolution: 1.99→2.061 Å / Redundancy: 1.9 % / Num. unique obs: 4641 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
iMOSFLM7.1.3data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MUS

5mus


Resolution: 1.99→63.93 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.06
RfactorNum. reflection% reflection
Rfree0.276 2326 5.07 %
Rwork0.2225 --
obs0.2253 45836 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.99→63.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5232 0 33 474 5739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085404
X-RAY DIFFRACTIONf_angle_d0.9357317
X-RAY DIFFRACTIONf_dihedral_angle_d14.3653292
X-RAY DIFFRACTIONf_chiral_restr0.051831
X-RAY DIFFRACTIONf_plane_restr0.006927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.03060.4241370.37312425X-RAY DIFFRACTION93
2.0306-2.07480.33971230.33962462X-RAY DIFFRACTION94
2.0748-2.12310.32641070.31862510X-RAY DIFFRACTION95
2.1231-2.17610.33771310.30912527X-RAY DIFFRACTION97
2.1761-2.2350.3381230.29492516X-RAY DIFFRACTION96
2.235-2.30080.37111260.27692515X-RAY DIFFRACTION96
2.3008-2.3750.29361510.25642590X-RAY DIFFRACTION99
2.375-2.45990.29751530.24832572X-RAY DIFFRACTION99
2.4599-2.55840.33951470.23212558X-RAY DIFFRACTION98
2.5584-2.67480.27741260.24282568X-RAY DIFFRACTION98
2.6748-2.81590.28871450.23142506X-RAY DIFFRACTION96
2.8159-2.99230.29481700.21212601X-RAY DIFFRACTION99
2.9923-3.22330.28471200.21612628X-RAY DIFFRACTION98
3.2233-3.54770.23281310.19572569X-RAY DIFFRACTION97
3.5477-4.0610.22881650.16552577X-RAY DIFFRACTION97
4.061-5.1160.2341240.15612667X-RAY DIFFRACTION98
5.116-63.96470.24521470.21532719X-RAY DIFFRACTION96

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