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- PDB-7ewu: Crystal structure of Ebinur Lake virus cap snatching endonuclease (WT) -

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Basic information

Entry
Database: PDB / ID: 7ewu
TitleCrystal structure of Ebinur Lake virus cap snatching endonuclease (WT)
ComponentsReplicase
KeywordsHYDROLASE / cap snatching 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: 2.11 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

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)101,05710
Polymers100,7284
Non-polymers3306
Water3,171176
1
A: Replicase


Theoretical massNumber of molelcules
Total (without water)25,1821
Polymers25,1821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9950 Å2
MethodPISA
2
B: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2923
Polymers25,1821
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-5 kcal/mol
Surface area9790 Å2
MethodPISA
3
C: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2923
Polymers25,1821
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-5 kcal/mol
Surface area9860 Å2
MethodPISA
4
D: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2923
Polymers25,1821
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-5 kcal/mol
Surface area9880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.812, 41.587, 145.313
Angle α, β, γ (deg.)90.000, 101.580, 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 / 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.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.08 Å3/Da / Density % sol: 40.89 %
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: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 47354 / % possible obs: 97.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 36.89 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.043 / Rrim(I) all: 0.096 / Χ2: 0.992 / Net I/σ(I): 10 / Num. measured all: 210591
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.11-2.194.60.56647580.8480.2860.6360.96199.2
2.19-2.273.60.40644270.8960.2250.4681.34892.4
2.27-2.384.80.38547330.9390.1890.4310.9599.5
2.38-2.54.60.26947620.9590.1350.3021.08499.6
2.5-2.664.60.18747950.9810.0930.2091.11999.4
2.66-2.864.70.14747980.9850.0720.1641.02799.8
2.86-3.154.50.09648460.9930.0490.1090.95399.9
3.15-3.614.50.07346770.9960.0360.0810.88997.1
3.61-4.544.30.06447040.9960.0320.0720.80496
4.54-504.10.05848540.9970.030.0660.86496.4

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XI5

2xi5


Resolution: 2.11→35.95 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2851 2340 4.97 %
Rwork0.24 44756 -
obs0.2422 47096 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.76 Å2 / Biso mean: 45.2921 Å2 / Biso min: 21.01 Å2
Refinement stepCycle: final / Resolution: 2.11→35.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5687 0 6 176 5869
Biso mean--64.81 43.2 -
Num. residues----721
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.11-2.150.29711170.29142607272496
2.15-2.20.33721360.31152686282299
2.2-2.250.48551400.43092257239788
2.25-2.310.43771310.33732540267193
2.31-2.370.35321350.29232640277599
2.37-2.440.3371220.268627322854100
2.44-2.520.311490.265926322781100
2.52-2.610.33011660.26052672283899
2.61-2.710.30771330.257226502783100
2.71-2.840.29521560.26526942850100
2.84-2.990.27881400.258426792819100
2.99-3.170.31121370.244227172854100
3.17-3.420.27441250.240727322857100
3.42-3.760.26791250.22582448257389
3.76-4.310.24981310.19422675280699
4.31-5.420.24121620.19822703286599
5.42-35.950.24711350.22142692282794

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