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- PDB-7ewy: Crystal structure of Ebinur Lake virus cap snatching endonuclease... -

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Basic information

Entry
Database: PDB / ID: 7ewy
TitleCrystal structure of Ebinur Lake virus cap snatching endonuclease (D79A mutant)
ComponentsReplicase
KeywordsHYDROLASE / endonuclease
Function / homology
Function and homology information


host cell / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / metal ion binding
Similarity search - Function
: / Virus, RNA-directed RNA polymerase L, thumb ring 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
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesAbbey lake orthobunyavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsKuang, W. / Hu, Z. / Gong, P.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0507200 China
Chinese Academy of Sciences2020-NBL-ZD-00030 China
CitationJournal: J.Virol. / Year: 2022
Title: Insights into Two-Metal-Ion Catalytic Mechanism of Cap-Snatching Endonuclease of Ebinur Lake Virus in Bunyavirales.
Authors: Kuang, W. / Zhang, H. / Cai, Y. / Zhang, G. / Deng, F. / Li, H. / Hu, Z. / Guo, Y. / Wang, M. / Zhou, Y. / Gong, P.
History
DepositionMay 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
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Revision 1.2Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicase
B: Replicase
C: Replicase
D: Replicase


Theoretical massNumber of molelcules
Total (without water)100,5514
Polymers100,5514
Non-polymers00
Water5,116284
1
A: Replicase


Theoretical massNumber of molelcules
Total (without water)25,1381
Polymers25,1381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Replicase


Theoretical massNumber of molelcules
Total (without water)25,1381
Polymers25,1381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Replicase


Theoretical massNumber of molelcules
Total (without water)25,1381
Polymers25,1381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Replicase


Theoretical massNumber of molelcules
Total (without water)25,1381
Polymers25,1381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.171, 69.670, 72.751
Angle α, β, γ (deg.)90.090, 89.980, 90.020
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Replicase / Transcriptase / L protein


Mass: 25137.865 Da / Num. of mol.: 4 / Fragment: N-terminal endonuclease domain / Mutation: D79A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Abbey lake orthobunyavirus / Strain: Cu20-XJ / Gene: RdRp / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A059WLS9, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 4.9 / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.01→69.64 Å / Num. obs: 52745 / % possible obs: 98 % / Redundancy: 3.6 % / Biso Wilson estimate: 29.56 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
2.01-2.063.10.7993879196.8
8.99-69.643.50.076587198.5

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XI5

2xi5


Resolution: 2.01→25.39 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 2385 4.56 %
Rwork0.2051 49930 -
obs0.2068 52315 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.03 Å2 / Biso mean: 33.921 Å2 / Biso min: 18.53 Å2
Refinement stepCycle: final / Resolution: 2.01→25.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5368 0 0 284 5652
Biso mean---38.42 -
Num. residues----683
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.01-2.050.3131670.25152807297493
2.05-2.10.25211890.22482795298495
2.1-2.140.27541440.22662897304196
2.14-2.20.25771170.22292896301396
2.2-2.260.27861230.22762930305397
2.26-2.320.27191430.22052960310397
2.32-2.40.28631290.22232917304697
2.4-2.480.27491280.2312940306897
2.48-2.580.26071090.22623003311298
2.58-2.70.31481550.22592951310698
2.7-2.840.28391320.2292918305098
2.84-3.020.2371460.22323022316898
3.02-3.250.23171520.20872936308899
3.25-3.580.22461360.19692975311199
3.58-4.10.19821390.18183013315299
4.1-5.150.19971710.16842953312499
5.16-25.390.26091050.20233017312299

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