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

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Basic information

Entry
Database: PDB / ID: 7ewv
TitleCrystal structure of Ebinur Lake virus cap snatching endonuclease (H34A 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: 2.61 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)50,3394
Polymers50,2302
Non-polymers1102
Water45025
1
A: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1702
Polymers25,1151
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-3 kcal/mol
Surface area9410 Å2
MethodPISA
2
B: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1702
Polymers25,1151
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-4 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.754, 41.009, 75.018
Angle α, β, γ (deg.)90.000, 99.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Replicase / Transcriptase / L protein


Mass: 25114.805 Da / Num. of mol.: 2 / Fragment: N-terminal endonuclease domain / Mutation: H34A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.14 Å3/Da / Density % sol: 42.39 % / Mosaicity: 1.217 °
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: 2.61→50 Å / Num. obs: 11695 / % possible obs: 88.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 45.36 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.047 / Rrim(I) all: 0.099 / Χ2: 0.967 / Net I/σ(I): 11.2 / Num. measured all: 39969
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.61-2.73.30.43711780.7950.2510.5080.99689.1
2.7-2.813.40.34211600.8810.1910.3951.01190.5
2.81-2.943.40.26812110.940.150.3091.0890.9
2.94-3.093.30.19511780.9460.1090.2251.05290.2
3.09-3.293.30.13211790.9720.0750.1541.02889.4
3.29-3.543.50.10311750.9880.0550.1170.92989.9
3.54-3.93.60.07811740.9940.0410.0890.92688.4
3.9-4.463.40.06211520.9930.0330.0710.90186.4
4.46-5.623.50.05911510.9960.030.0670.90886.8
5.62-503.40.05411370.9980.030.0620.85180.9

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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: 2.61→29.64 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 574 4.92 %
Rwork0.2255 11088 -
obs0.2266 11662 88.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123 Å2 / Biso mean: 48.8069 Å2 / Biso min: 28.02 Å2
Refinement stepCycle: final / Resolution: 2.61→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 2 25 2679
Biso mean--103.18 42.11 -
Num. residues----347
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 (%)
2.61-2.870.3481380.28782791292990
2.87-3.290.31121370.24992827296490
3.29-4.140.23521550.2142759291489
4.14-29.640.21311440.20652711285584

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