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- PDB-7ex1: Crystal structure of Ebinur Lake virus cap snatching endonuclease... -

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Basic information

Entry
Database: PDB / ID: 7ex1
TitleCrystal structure of Ebinur Lake virus cap snatching endonuclease (Y109A 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: 2.3 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

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Assembly

Deposited unit
A: Replicase
B: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2504
Polymers50,1802
Non-polymers712
Water1,06359
1
A: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1252
Polymers25,0901
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area9500 Å2
MethodPISA
2
B: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1252
Polymers25,0901
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area9390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.528, 40.812, 74.577
Angle α, β, γ (deg.)90.000, 100.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Replicase / Transcriptase / L protein


Mass: 25089.779 Da / Num. of mol.: 2 / Fragment: N-terminal endonuclease domain / Mutation: Y109A
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-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.13 Å3/Da / Density % sol: 42.26 % / Mosaicity: 0.57 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 5 / 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 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18574 / % possible obs: 97 % / Redundancy: 3.9 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.052 / Rrim(I) all: 0.106 / Χ2: 0.963 / Net I/σ(I): 8.6 / Num. measured all: 72606
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.383.80.48318700.8590.270.5570.96598.6
2.38-2.484.10.40618740.8640.2190.4630.96799.3
2.48-2.594.10.29318630.9240.1590.3351.02499.3
2.59-2.734.10.23118680.9470.1250.2641.07197.3
2.73-2.94.20.17418670.9770.0940.1991.02998.7
2.9-3.123.90.12318620.9840.0670.1411.01198.2
3.12-3.4440.08518780.990.0460.0970.90597.9
3.44-3.933.80.06918530.9920.0390.080.92696.6
3.93-4.953.70.06518310.9920.0370.0750.89694.4
4.95-503.50.06918080.9940.0410.0810.78790.4

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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: 2.3→46.5 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2555 846 4.56 %
Rwork0.2202 17697 -
obs0.2219 18543 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.05 Å2 / Biso mean: 48.3128 Å2 / Biso min: 27.41 Å2
Refinement stepCycle: final / Resolution: 2.3→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2655 0 2 59 2716
Biso mean--32.71 48.8 -
Num. residues----340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.440.3281350.26632942307798
2.44-2.630.28561370.25282990312799
2.63-2.90.32491650.24932954311998
2.9-3.320.26561140.22542988310298
3.32-4.180.24081210.2052995311697
4.18-46.50.22991740.20592828300291

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