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- PDB-7ex4: Crystal structure of Ebinur Lake virus cap snatching endonuclease... -

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Basic information

Entry
Database: PDB / ID: 7ex4
TitleCrystal structure of Ebinur Lake virus cap snatching endonuclease in complex with inhibitor 5
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
Chem-IA5 / : / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesAbbey lake orthobunyavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: Structural and Biochemical Basis for Development of Diketo Acid Inhibitors Targeting the Cap-Snatching Endonuclease of the Ebinur Lake Virus (Order: Bunyavirales ).
Authors: Kuang, W. / Zhang, H. / Cai, Y. / Zhang, G. / Deng, F. / Li, H. / Zhou, Y. / Wang, M. / Gong, P. / Guo, Y. / Hu, Z.
History
DepositionMay 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 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 27, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8696
Polymers25,1821
Non-polymers6885
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.933, 70.566, 70.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25181.875 Da / Num. of mol.: 1 / Fragment: N-terminal endonuclease domain
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-IA5 / methyl (Z)-4-(1-(3-bromobenzyl)-4-(4-chlorobenzyl)piperidin-4-yl)-2-hydroxy-4-oxobut-2-enoate


Mass: 506.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25BrClNO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.49 % / Mosaicity: 1.293 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 5.1 / 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: Jan 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 12910 / % possible obs: 88.5 % / Redundancy: 3 % / Biso Wilson estimate: 26.99 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.071 / Rrim(I) all: 0.127 / Χ2: 0.992 / Net I/σ(I): 10 / Num. measured all: 39371
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.073.40.34411620.8510.2060.4030.88684.1
2.07-2.153.40.26312910.9090.1590.310.93787.4
2.15-2.253.30.24112600.9180.1490.2850.98290.6
2.25-2.373.20.19713170.9280.1260.2351.0291.3
2.37-2.523.20.17313450.950.1090.2061.00893
2.52-2.713.10.13513300.9640.0890.1621.00990.8
2.71-2.992.90.10213060.9760.0690.1241.03391.2
2.99-3.422.70.08812940.980.0620.1081.06587.6
3.42-4.312.60.08312760.980.0570.1011.02585.8
4.31-502.80.07813290.9930.0560.0970.98984

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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→35.41 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 623 4.87 %
Rwork0.2052 12180 -
obs0.2067 12803 88.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.37 Å2 / Biso mean: 30.7053 Å2 / Biso min: 18.62 Å2
Refinement stepCycle: final / Resolution: 2→35.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1431 0 35 93 1559
Biso mean--37.99 34.84 -
Num. residues----181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.20.28891580.20952931308987
2.2-2.520.24581580.21423102326092
2.52-3.170.27751660.22453094326091
3.17-35.410.20031410.19263053319485

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