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- PDB-7ex8: Crystal structure of Ebinur Lake virus cap snatching endonuclease... -

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Basic information

Entry
Database: PDB / ID: 7ex8
TitleCrystal structure of Ebinur Lake virus cap snatching endonuclease in complex with inhibitor 27
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
Chem-I27 / : / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesAbbey lake orthobunyavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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

Downloads & links

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Assembly

Deposited unit
A: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8607
Polymers25,1821
Non-polymers6796
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.748, 70.692, 71.063
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 / 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-I27 / methyl (Z)-4-[1-[(3-chlorophenyl)methyl]-4-[(4-chlorophenyl)methyl]piperidin-4-yl]-2-oxidanyl-4-oxidanylidene-but-2-enoate


Mass: 462.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25Cl2NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 82 / 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: 39.48 % / Mosaicity: 0.949 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 4.7 / 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 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 14633 / % possible obs: 96.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 29.73 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.048 / Rrim(I) all: 0.107 / Χ2: 0.935 / Net I/σ(I): 8.9 / Num. measured all: 70936
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.97-2.043.40.40812320.8920.2390.4760.84582.7
2.04-2.124.10.35513290.910.1890.4040.8991
2.12-2.224.40.31414490.9390.1610.3550.88498.2
2.22-2.344.80.27414880.9530.1380.3090.91199.8
2.34-2.485.50.23314870.9810.1080.2570.88799.8
2.48-2.675.40.15414880.9870.0720.170.9599.7
2.67-2.945.30.11215150.9930.0540.1250.98399.7
2.94-3.375.30.07815140.9940.0380.0870.95399.7
3.37-4.245.30.07615110.9920.0370.0850.9799.2
4.24-504.60.07216200.9930.0380.0821.00898.1

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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: 1.97→26.78 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 710 4.87 %
Rwork0.1951 13858 -
obs0.1967 14568 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.36 Å2 / Biso mean: 33.918 Å2 / Biso min: 19.99 Å2
Refinement stepCycle: final / Resolution: 1.97→26.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1437 0 28 82 1547
Biso mean--35.63 38.88 -
Num. residues----180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.97-2.120.27191210.22852407252886
2.12-2.340.2581440.20332796294099
2.34-2.670.24691550.199228132968100
2.67-3.370.2441390.202528873026100
3.37-26.780.20091510.1842955310699

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