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- PDB-6qhg: Structure of the cap-binding domain of Rift Valley Fever virus L ... -

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Basic information

Entry
Database: PDB / ID: 6qhg
TitleStructure of the cap-binding domain of Rift Valley Fever virus L protein
ComponentsPolymerase
KeywordsVIRAL PROTEIN / Bunyavirus / viral polymerase / cap-binding / viral transcription
Function / homology
Function and homology information


nucleoside binding / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription
Similarity search - Function
RNA-directed RNA polymerase, phlebovirus / RNA-directed RNA polymerase L, PA-C-like domain / RNA-directed RNA polymerase L, PA-C-like domain / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / 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 / PHOSPHATE ION / Replicase
Similarity search - Component
Biological speciesRift valley fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.483 Å
AuthorsGogrefe, N. / Reindl, S. / Gunther, S. / Rosenthal, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationRE 3712/1-1 Germany
Germany
CitationJournal: Plos Pathog. / Year: 2019
Title: Structure of a functional cap-binding domain in Rift Valley fever virus L protein.
Authors: Gogrefe, N. / Reindl, S. / Gunther, S. / Rosenthal, M.
History
DepositionJan 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase
B: Polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6757
Polymers27,3182
Non-polymers1,3585
Water7,224401
1
A: Polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2903
Polymers13,6591
Non-polymers6312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3854
Polymers13,6591
Non-polymers7263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.580, 53.681, 135.987
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 Polymerase


Mass: 13658.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift valley fever virus / Production host: Escherichia coli (E. coli) / References: UniProt: F4ZDJ0
#2: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20N5O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 24% PEG 2000 MME, 200 mM Trimethylamine N-oxide, 2 mM TCEP, 5 mM dithiothreitol, 2 mM m7GTP and 100 mM Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.483→67.99 Å / Num. obs: 39006 / % possible obs: 99 % / Redundancy: 12 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.048 / Rrim(I) all: 0.123 / Net I/σ(I): 10
Reflection shellResolution: 1.483→1.536 Å / Rmerge(I) obs: 0.403 / Rpim(I) all: 0.168 / Rrim(I) all: 0.437

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.483→42.133 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 16.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1935 1888 4.85 %
Rwork0.1519 --
obs0.1539 38899 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.483→42.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 83 401 2369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062049
X-RAY DIFFRACTIONf_angle_d0.9042792
X-RAY DIFFRACTIONf_dihedral_angle_d18.068752
X-RAY DIFFRACTIONf_chiral_restr0.081271
X-RAY DIFFRACTIONf_plane_restr0.005353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.483-1.52310.21791250.15142780X-RAY DIFFRACTION98
1.5231-1.56790.19921350.14162799X-RAY DIFFRACTION98
1.5679-1.61850.19781440.1372769X-RAY DIFFRACTION98
1.6185-1.67640.19261330.14162820X-RAY DIFFRACTION98
1.6764-1.74350.18121330.14322801X-RAY DIFFRACTION99
1.7435-1.82280.20911500.1422787X-RAY DIFFRACTION99
1.8228-1.91890.17321530.13762812X-RAY DIFFRACTION99
1.9189-2.03920.15971420.14742800X-RAY DIFFRACTION98
2.0392-2.19660.22191420.14932875X-RAY DIFFRACTION100
2.1966-2.41760.2131610.15062879X-RAY DIFFRACTION100
2.4176-2.76740.21251580.1662850X-RAY DIFFRACTION99
2.7674-3.48640.16971520.15872963X-RAY DIFFRACTION100
3.4864-42.14960.19041600.16763076X-RAY DIFFRACTION100

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