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- PDB-7v3b: Crystal structure of NP exonuclease C409A-PCMPS complex -

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Basic information

Entry
Database: PDB / ID: 7v3b
TitleCrystal structure of NP exonuclease C409A-PCMPS complex
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / DEDDh exonuclease / NP exonuclease / anti-viral drug / PCMPS / PCMB
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / 3'-5' exonuclease activity / viral nucleocapsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / ribonucleoprotein complex ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / 3'-5' exonuclease activity / viral nucleocapsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / ribonucleoprotein complex / RNA binding / metal ion binding / identical protein binding
Similarity search - Function
Nucleocapsid protein, arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, C-terminal superfamily / Arenavirus nucleocapsid N-terminal domain / Arenavirus nucleocapsid C-terminal domain / WD40 repeat
Similarity search - Domain/homology
PARA-MERCURY-BENZENESULFONIC ACID / Nucleoprotein
Similarity search - Component
Biological speciesLassa virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsHsiao, Y.Y. / Huang, K.W.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST103-2311-B-009-001-MY3 Taiwan
Ministry of Science and Technology (MoST, Taiwan)MOST108-2636-B-009-004 Taiwan
CitationJournal: Jacs Au / Year: 2021
Title: Targeted Covalent Inhibitors Allosterically Deactivate the DEDDh Lassa Fever Virus NP Exonuclease from Alternative Distal Sites.
Authors: Huang, K.W. / Chen, J.W. / Hua, T.Y. / Chu, Y.Y. / Chiu, T.Y. / Liu, J.Y. / Tu, C.I. / Hsu, K.C. / Kao, Y.T. / Chu, J.W. / Hsiao, Y.Y.
History
DepositionAug 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 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: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8607
Polymers55,3232
Non-polymers5375
Water5,242291
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1094
Polymers27,6621
Non-polymers4473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area11280 Å2
MethodPISA
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7513
Polymers27,6621
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.703, 58.897, 69.188
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 27661.574 Da / Num. of mol.: 2 / Mutation: C409A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)
Strain: Mouse/Sierra Leone/Josiah/1976 / Production host: Escherichia coli (E. coli)
References: UniProt: P13699, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PMB / PARA-MERCURY-BENZENESULFONIC ACID


Mass: 357.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5HgO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350, 2 mM Sodium p-chloromercuriphenylsulphonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.99258 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99258 Å / Relative weight: 1
ReflectionResolution: 1.795→30 Å / Num. obs: 47519 / % possible obs: 99.8 % / Redundancy: 11.1 % / Biso Wilson estimate: 25.39 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.019 / Rrim(I) all: 0.065 / Χ2: 1.011 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8610.40.49746540.9370.1590.5220.37699.8
1.86-1.9410.80.36546800.9690.1150.3830.41799.8
1.94-2.0310.90.25346870.9850.0790.2650.47599.9
2.03-2.1311.10.18947120.9910.0580.1980.53699.9
2.13-2.2711.30.13647020.9950.0420.1430.645100
2.27-2.4411.50.10147340.9970.0310.1060.736100
2.44-2.6911.50.08347560.9980.0250.0870.928100
2.69-3.0811.50.07147570.9980.0220.0741.512100
3.08-3.8811.40.0548170.9990.0150.0531.97899.8
3.88-3011.10.0450200.9990.0120.0422.28899.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD
Starting model: 4G9Z

4g9z


Resolution: 1.8→29.829 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 21.19
RfactorNum. reflection% reflection
Rfree0.2184 3682 7.76 %
Rwork0.186 --
obs0.1885 47464 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.22 Å2 / Biso mean: 34.2104 Å2 / Biso min: 13.38 Å2
Refinement stepCycle: final / Resolution: 1.8→29.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 15 291 3552
Biso mean--30.13 39.68 -
Num. residues----414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.81830.30151410.2388154194
1.8183-1.84330.25991310.22861663100
1.8433-1.86960.25841200.21951687100
1.8696-1.89750.25921640.20671636100
1.8975-1.92710.23161330.2071669100
1.9271-1.95870.26961390.1941675100
1.9587-1.99250.22441390.1931644100
1.9925-2.02870.22181610.18381679100
2.0287-2.06770.2081290.19071665100
2.0677-2.10990.20711330.18451690100
2.1099-2.15580.19621090.18941698100
2.1558-2.20590.21181470.18451653100
2.2059-2.26110.2211560.18631665100
2.2611-2.32220.20611500.18741667100
2.3222-2.39050.22071390.19121695100
2.3905-2.46760.24531340.19511690100
2.4676-2.55570.26231500.19751678100
2.5557-2.6580.23521510.19551683100
2.658-2.77890.24411390.19911697100
2.7789-2.92530.25381440.20171690100
2.9253-3.10840.2311140.20271715100
3.1084-3.34810.25311480.19331697100
3.3481-3.68450.18411610.18041701100
3.6845-4.21640.19011420.1561729100
4.2164-5.30730.18991540.16521746100
5.3073-29.8290.20581540.1825182999
Refinement TLS params.Method: refined / Origin x: 25.7411 Å / Origin y: 29.5448 Å / Origin z: 30.2572 Å
111213212223313233
T0.2069 Å20.0124 Å2-0.0042 Å2-0.1476 Å2-0.002 Å2--0.1272 Å2
L2.2293 °20.7004 °2-0.0333 °2-0.2406 °2-0.0196 °2--0.0421 °2
S0.0324 Å °-0.0167 Å °0.042 Å °0.0128 Å °-0.0044 Å °0.0027 Å °-0.0018 Å °0.0073 Å °-0.0285 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA363 - 569
2X-RAY DIFFRACTION1allB363 - 569
3X-RAY DIFFRACTION1allD1 - 3
4X-RAY DIFFRACTION1allE1
5X-RAY DIFFRACTION1allC1 - 2
6X-RAY DIFFRACTION1allS1 - 357

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