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

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Basic information

Entry
Database: PDB / ID: 7ewz
TitleCrystal structure of Ebinur Lake virus cap snatching endonuclease (D92A mutant)
ComponentsReplicaseRNA-dependent RNA polymerase
KeywordsHYDROLASE / endonuclease
Function / homology
Function and homology information


host cell endoplasmic reticulum / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent 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: 2.05 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
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
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

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Assembly

Deposited unit
A: Replicase
B: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4576
Polymers50,2762
Non-polymers1814
Water93752
1
A: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2283
Polymers25,1381
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-14 kcal/mol
Surface area9740 Å2
MethodPISA
2
B: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2283
Polymers25,1381
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-15 kcal/mol
Surface area9530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.871, 72.189, 71.868
Angle α, β, γ (deg.)90.000, 90.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Replicase / RNA-dependent RNA polymerase / Transcriptase / L protein


Mass: 25137.865 Da / Num. of mol.: 2 / Fragment: N-terminal endonuclease domain / Mutation: D92A
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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.11 Å3/Da / Density % sol: 41.67 % / Mosaicity: 1.352 °
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: Jun 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 24961 / % possible obs: 94.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 43.38 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.038 / Rrim(I) all: 0.087 / Χ2: 0.979 / Net I/σ(I): 12.2 / Num. measured all: 130729
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.124.70.54920140.910.2490.6050.83376.5
2.12-2.214.80.47222110.9320.2170.5220.84784.7
2.21-2.314.80.32623740.9670.1550.3630.95790
2.31-2.435.30.30425650.9640.140.3360.98497.8
2.43-2.585.60.25526140.9780.1170.2821.04599.2
2.58-2.785.40.18226170.9850.0870.2021.03599.7
2.78-3.065.70.12126310.9930.0560.1341.02499.9
3.06-3.515.30.07226270.9960.0350.080.92199.5
3.51-4.425.50.05826430.9960.0270.0641.02599.3
4.42-5050.06126650.9940.0310.0691.02198.4

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XI5

2xi5


Resolution: 2.05→27.05 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2713 1273 5.12 %
Rwork0.2266 23574 -
obs0.2289 24847 94.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.29 Å2 / Biso mean: 52.0491 Å2 / Biso min: 31.44 Å2
Refinement stepCycle: final / Resolution: 2.05→27.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 4 52 2773
Biso mean--67.53 53.3 -
Num. residues----346
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.130.37551150.30922135225077
2.13-2.230.37981450.30722332247785
2.23-2.350.3321190.28252528264792
2.35-2.490.31681390.27992745288499
2.49-2.690.32681760.25832735291199
2.69-2.960.27741560.259527612917100
2.96-3.380.30671380.239727592897100
3.38-4.260.2451430.20622778292199
4.26-27.050.23511420.1972801294398

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