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- PDB-7ex7: Crystal structure of Ebinur Lake virus cap snatching endonuclease... -

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Basic information

Entry
Database: PDB / ID: 7ex7
TitleCrystal structure of Ebinur Lake virus cap snatching endonuclease in complex with inhibitor 16
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-1I6 / : / 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: 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
B: Replicase
C: Replicase
D: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,03417
Polymers100,7284
Non-polymers2,30713
Water3,891216
1
A: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7504
Polymers25,1821
Non-polymers5683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-5 kcal/mol
Surface area9580 Å2
MethodPISA
2
B: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7504
Polymers25,1821
Non-polymers5683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-5 kcal/mol
Surface area9560 Å2
MethodPISA
3
C: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7855
Polymers25,1821
Non-polymers6034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-17 kcal/mol
Surface area9610 Å2
MethodPISA
4
D: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7504
Polymers25,1821
Non-polymers5683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-5 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.272, 41.676, 145.305
Angle α, β, γ (deg.)90.000, 102.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Replicase / Transcriptase / L protein


Mass: 25181.875 Da / Num. of mol.: 4 / 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.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-1I6 / methyl (Z)-4-(4-(4-chlorobenzyl)-1-(3-methoxybenzyl)piperidin-4-yl)-2-hydroxy-4-oxobut-2-enoate


Mass: 457.947 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H28ClNO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.07 Å3/Da / Density % sol: 40.46 % / Mosaicity: 0.443 °
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: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 33393 / % possible obs: 89.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.84 Å2 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.075 / Rrim(I) all: 0.152 / Χ2: 1.055 / Net I/σ(I): 5.8 / Num. measured all: 122217
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.383.40.49432610.8080.2910.5771.02588.3
2.38-2.483.70.42434760.8540.2410.4911.02893.1
2.48-2.593.70.33833950.8910.1940.3931.07992.4
2.59-2.733.60.27733780.9120.1620.3231.08990.8
2.73-2.93.80.2333800.9490.1310.2661.191.7
2.9-3.123.70.15933220.9760.0910.1841.03189.3
3.12-3.443.80.11533710.9860.0650.1331.06389.9
3.44-3.933.60.08432960.9920.0490.0981.03388.2
3.93-4.953.60.06532430.9940.0380.0761.03485.7
4.95-503.60.07132710.9970.0410.0831.05883.5

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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→44.94 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 1696 5.1 %
Rwork0.2085 31558 -
obs0.2114 33254 89.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.73 Å2 / Biso mean: 32.8099 Å2 / Biso min: 12.89 Å2
Refinement stepCycle: final / Resolution: 2.3→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5510 0 137 216 5863
Biso mean--31.89 33.11 -
Num. residues----701
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.370.30421320.25282571270388
2.37-2.440.30641470.24922719286693
2.44-2.530.3471390.24982689282893
2.53-2.630.31341570.22962694285192
2.63-2.750.30231410.23562651279291
2.75-2.90.28971550.22742646280191
2.9-3.080.28141580.21272619277790
3.08-3.320.26971370.2122627276489
3.32-3.650.26351350.19392649278489
3.65-4.180.22261350.17512618275388
4.18-5.260.20061210.17812544266585
5.26-44.940.25691390.2122531267082

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