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- PDB-7ex0: Crystal structure of Ebinur Lake virus cap snatching endonuclease... -

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Basic information

Entry
Database: PDB / ID: 7ex0
TitleCrystal structure of Ebinur Lake virus cap snatching endonuclease (K108A 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: 2.07 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)50,4676
Polymers50,2482
Non-polymers2204
Water3,441191
1
A: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2343
Polymers25,1241
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-12 kcal/mol
Surface area10050 Å2
MethodPISA
2
B: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2343
Polymers25,1241
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-12 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.808, 41.452, 85.766
Angle α, β, γ (deg.)90.000, 104.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Replicase / Transcriptase / L protein


Mass: 25123.773 Da / Num. of mol.: 2 / Fragment: N-terminal endonuclease domain / Mutation: K108A
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.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.39 Å3/Da / Density % sol: 48.5 % / Mosaicity: 0.883 °
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: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 29345 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 35.91 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.024 / Rrim(I) all: 0.047 / Χ2: 0.935 / Net I/σ(I): 15.3 / Num. measured all: 104989
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.07-2.143.60.45528610.8370.2730.5330.92299.7
2.14-2.233.70.32929120.8940.1970.3850.915100
2.23-2.333.50.2529380.9230.1540.2950.986100
2.33-2.453.60.17229120.9660.1040.2020.96199.9
2.45-2.613.60.11529210.9860.0690.1350.93199.9
2.61-2.813.50.07729260.9930.0470.090.999.8
2.81-3.093.70.05129240.9970.0310.0590.897100
3.09-3.543.60.0329500.9990.0180.0350.926100
3.54-4.463.60.02129640.9990.0130.0240.90899.8
4.46-503.40.02130370.9990.0130.0251.01598.9

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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: 2.07→30.21 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 1444 4.93 %
Rwork0.2028 27843 -
obs0.2042 29287 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.69 Å2 / Biso mean: 41.8006 Å2 / Biso min: 20.48 Å2
Refinement stepCycle: final / Resolution: 2.07→30.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 4 191 3031
Biso mean--76.91 43.86 -
Num. residues----353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.07-2.140.34041400.28112717285799
2.14-2.230.28881330.252227672900100
2.23-2.330.29151380.244628102948100
2.33-2.450.25651590.231727382897100
2.45-2.610.27411420.223227742916100
2.61-2.810.2771270.22627952922100
2.81-3.090.29021650.233127602925100
3.09-3.540.22451390.2128082947100
3.54-4.460.18971450.173328132958100
4.46-30.210.18841560.16992861301799

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