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- PDB-7v3c: Crystal structure of NP exonuclease C409A-PCMB complex -

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Basic information

Entry
Database: PDB / ID: 7v3c
TitleCrystal structure of NP exonuclease C409A-PCMB 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 / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / 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 / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / 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
4-(HYDROXYMERCURY)BENZOIC ACID / Nucleoprotein
Similarity search - Component
Biological speciesLassa virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)55,8417
Polymers55,3232
Non-polymers5185
Water3,477193
1
A: 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 area100 Å2
ΔGint-7 kcal/mol
Surface area10750 Å2
MethodPISA
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0904
Polymers27,6621
Non-polymers4283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-8 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.851, 58.809, 68.845
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HGB / 4-(HYDROXYMERCURY)BENZOIC ACID


Mass: 338.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6HgO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350, 2 mM Sodium p-hydroxymercuribenzoate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.99263 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: 0.99263 Å / Relative weight: 1
ReflectionResolution: 1.896→30 Å / Num. obs: 40392 / % possible obs: 99.6 % / Redundancy: 9.2 % / Biso Wilson estimate: 33.11 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.019 / Rrim(I) all: 0.061 / Χ2: 1.306 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.976.70.47639780.7190.1880.5140.44999.5
1.97-2.057.60.36139610.8860.1330.3860.44599.8
2.05-2.1480.29439800.9330.1050.3120.59399.8
2.14-2.258.80.2140080.9750.070.2220.6699.8
2.25-2.399.20.15240030.9910.050.160.7599.7
2.39-2.589.70.11340090.9950.0360.1190.8999.7
2.58-2.84100.09240450.9970.0290.0961.29299.7
2.84-3.2510.30.0740570.9980.0220.0731.91599.8
3.25-4.0910.40.04740950.9990.0150.052.24799.6
4.09-3010.70.03842560.9990.0120.042.66498.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V37

7v37


Resolution: 1.9→26.438 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 22.77
RfactorNum. reflection% reflection
Rfree0.2216 3096 7.67 %
Rwork0.1869 --
obs0.1896 40356 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.16 Å2 / Biso mean: 44.1354 Å2 / Biso min: 18.55 Å2
Refinement stepCycle: final / Resolution: 1.9→26.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 14 193 3361
Biso mean--38.08 46.28 -
Num. residues----402
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92610.33281240.284155893
1.9261-1.95770.28951390.25571672100
1.9577-1.99140.27171340.23121671100
1.9914-2.02760.29691590.23911674100
2.0276-2.06660.3121390.22931669100
2.0666-2.10870.25041450.22741689100
2.1087-2.15460.30891400.20521667100
2.1546-2.20470.22891290.20761673100
2.2047-2.25980.21731380.19121708100
2.2598-2.32080.23281260.19291687100
2.3208-2.38910.27141350.19171688100
2.3891-2.46620.22551330.18741692100
2.4662-2.55420.21721210.20311728100
2.5542-2.65640.2681510.19521670100
2.6564-2.77720.28361460.20891694100
2.7772-2.92340.26221460.21571694100
2.9234-3.10630.27061430.21021709100
3.1063-3.34570.23861340.20541723100
3.3457-3.68160.19111340.16731721100
3.6816-4.21250.18541600.15751720100
4.2125-5.30030.15471490.14961763100
5.3003-26.4380.20491710.1751179098
Refinement TLS params.Method: refined / Origin x: 35.7503 Å / Origin y: 29.3036 Å / Origin z: -4.3306 Å
111213212223313233
T0.3083 Å20.0155 Å20.0004 Å2-0.1681 Å20.0183 Å2--0.1808 Å2
L3.8086 °20.9269 °20.2508 °2-0.2828 °20.1344 °2--0.2602 °2
S0.0066 Å °0.0212 Å °-0.0602 Å °0.0127 Å °0.0268 Å °0.0064 Å °-0.0235 Å °0.0033 Å °-0.0299 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA363 - 569
2X-RAY DIFFRACTION1allB363 - 569
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allE1
5X-RAY DIFFRACTION1allD1 - 2
6X-RAY DIFFRACTION1allS1 - 255

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