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- PDB-7oa4: Crystal structure of the N-terminal endonuclease domain of La Cro... -

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Basic information

Entry
Database: PDB / ID: 7oa4
TitleCrystal structure of the N-terminal endonuclease domain of La Crosse virus L-protein bound to compound L-742,001
ComponentsN-terminal endonuclease domain of La Crosse virus L-protein
KeywordsTRANSFERASE / complex / inhibitor / endonuclease
Function / homology
Function and homology information


host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity ...host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / RNA binding / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase, orthobunyavirus / : / 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-0N8 / FORMIC ACID / : / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesBunyavirus La Crosse
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFeracci, M. / Hernandez, S. / Vincentelli, R. / Ferron, F. / Reguera, J. / Canard, B. / Alvarez, K.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-ASTR-0010-01, PaNuVi France
CitationJournal: Iucrj / Year: 2024
Title: Biophysical and structural study of La Crosse virus endonuclease inhibition for the development of new antiviral options.
Authors: Feracci, M. / Hernandez, S. / Garlatti, L. / Mondielli, C. / Vincentelli, R. / Canard, B. / Reguera, J. / Ferron, F. / Alvarez, K.
History
DepositionApr 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: N-terminal endonuclease domain of La Crosse virus L-protein
BBB: N-terminal endonuclease domain of La Crosse virus L-protein
DDD: N-terminal endonuclease domain of La Crosse virus L-protein
GGG: N-terminal endonuclease domain of La Crosse virus L-protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,26222
Polymers86,8904
Non-polymers2,37118
Water1,838102
1
AAA: N-terminal endonuclease domain of La Crosse virus L-protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3386
Polymers21,7231
Non-polymers6165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
BBB: N-terminal endonuclease domain of La Crosse virus L-protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2925
Polymers21,7231
Non-polymers5704
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
DDD: N-terminal endonuclease domain of La Crosse virus L-protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3386
Polymers21,7231
Non-polymers6165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
GGG: N-terminal endonuclease domain of La Crosse virus L-protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2925
Polymers21,7231
Non-polymers5704
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.790, 124.790, 295.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
N-terminal endonuclease domain of La Crosse virus L-protein / Protein L / Large structural protein / Replicase / Transcriptase / RNA-directed RNA polymerase L


Mass: 21722.607 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bunyavirus La Crosse / Production host: Escherichia coli (E. coli)
References: UniProt: A5HC98, RNA-directed RNA polymerase, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-0N8 / (2Z)-4-[1-benzyl-4-(4-chlorobenzyl)piperidin-4-yl]-2-hydroxy-4-oxobut-2-enoic acid


Mass: 413.894 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H24ClNO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.83 Å3/Da / Density % sol: 67.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 3.4M Na-formate 0.1M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97563 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97563 Å / Relative weight: 1
ReflectionResolution: 2.9→108.071 Å / Num. obs: 31157 / % possible obs: 100 % / Redundancy: 27.8 % / Biso Wilson estimate: 49.67 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.043 / Rrim(I) all: 0.23 / Net I/σ(I): 13.2
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 27.09 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1505 / CC1/2: 0.909 / Rpim(I) all: 0.202 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia20.6.475-g7ac7bb6b-dials-2.2data reduction
DIALS2.2.10-g6dafd9427-releasedata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XI7

2xi7


Resolution: 2.9→108.071 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.164 / SU B: 13.152 / SU ML: 0.23 / Average fsc free: 0.9081 / Average fsc work: 0.9253 / Cross valid method: FREE R-VALUE / ESU R: 0.736 / ESU R Free: 0.327
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2386 1542 4.963 %
Rwork0.197 29531 -
all0.199 --
obs-31073 99.981 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 52.961 Å2
Baniso -1Baniso -2Baniso -3
1-0.393 Å20.197 Å20 Å2
2--0.393 Å2-0 Å2
3----1.276 Å2
Refinement stepCycle: LAST / Resolution: 2.9→108.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6132 0 142 102 6376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136409
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176004
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.6488710
X-RAY DIFFRACTIONr_angle_other_deg1.0841.58413803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7685734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22822.418397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.762151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3431544
X-RAY DIFFRACTIONr_chiral_restr0.0460.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021502
X-RAY DIFFRACTIONr_nbd_refined0.1830.21227
X-RAY DIFFRACTIONr_symmetry_nbd_other0.160.25501
X-RAY DIFFRACTIONr_nbtor_refined0.1630.23142
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.23257
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2153
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0620.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1280.221
X-RAY DIFFRACTIONr_nbd_other0.1590.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2210.211
X-RAY DIFFRACTIONr_mcbond_it1.3025.5662945
X-RAY DIFFRACTIONr_mcbond_other1.3025.5662946
X-RAY DIFFRACTIONr_mcangle_it2.2378.343676
X-RAY DIFFRACTIONr_mcangle_other2.2378.3423677
X-RAY DIFFRACTIONr_scbond_it1.4115.7483464
X-RAY DIFFRACTIONr_scbond_other1.4115.7483463
X-RAY DIFFRACTIONr_scangle_it2.4968.5665034
X-RAY DIFFRACTIONr_scangle_other2.4968.5675035
X-RAY DIFFRACTIONr_lrange_it5.296104.62225898
X-RAY DIFFRACTIONr_lrange_other5.294104.65425871
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.9-2.9750.3511160.29521450.29822670.810.8499.73530.267
2.975-3.0570.34980.2820740.28321720.8320.851000.251
3.057-3.1450.3521000.28920270.29221270.8290.8541000.257
3.145-3.2420.3121120.26719490.26920610.8650.8861000.235
3.242-3.3480.334980.24318970.24719950.8590.9141000.212
3.348-3.4660.27950.23718740.23919690.9060.9211000.205
3.466-3.5960.2411010.20417750.20618760.9340.9481000.178
3.596-3.7430.234720.20217450.20318170.9410.9481000.175
3.743-3.9090.26990.20516630.20817620.9170.9371000.182
3.909-4.10.213840.18315750.18516590.9440.9561000.162
4.1-4.3210.225720.17315470.17616190.9450.9591000.149
4.321-4.5830.181760.15514400.15715160.9620.9681000.135
4.583-4.8990.165720.15213590.15314310.9670.971000.131
4.899-5.290.176800.15312720.15513520.9740.9721000.131
5.29-5.7940.279510.17111910.17612420.9570.9681000.148
5.794-6.4750.222630.18110810.18311440.9460.9591000.159
6.475-7.4730.247500.1689820.17110320.9220.9671000.146
7.473-9.1410.183480.1548300.1568780.9670.9711000.14
9.141-12.8810.147280.136830.1317110.9820.9851000.124
12.881-108.0710.276270.2724210.2724480.9460.931000.26

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