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- PDB-7v3a: Crystal structure of apo-NP exonuclease C409A -

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Basic information

Entry
Database: PDB / ID: 7v3a
TitleCrystal structure of apo-NP exonuclease C409A
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
Biological speciesLassa virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.1Mar 23, 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_DOI / _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)55,5036
Polymers55,3232
Non-polymers1794
Water5,819323
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 area11270 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 area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.324, 59.431, 71.533
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium formate dihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 33231 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 31.19 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.038 / Rrim(I) all: 0.097 / Χ2: 1.593 / Net I/σ(I): 8.6 / Num. measured all: 215047
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.185.50.44732550.8890.2020.4920.66599.5
2.18-2.265.90.38532650.9230.170.4220.84999.9
2.26-2.376.40.32632690.9590.1390.3550.975100
2.37-2.496.80.25532960.9710.1060.2771.07499.9
2.49-2.6570.21832980.9780.0890.2361.27399.9
2.65-2.8570.15433020.990.0630.1671.51899.9
2.85-3.146.90.1233090.9920.0490.131.86899.8
3.14-3.596.60.07933310.9970.0340.0862.42399.5
3.59-4.526.20.0633660.9970.0260.0652.65899.7
4.52-306.50.04735400.9980.020.0522.33599.7

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Processing

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

7v37


Resolution: 2.1→29.794 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.48
RfactorNum. reflection% reflection
Rfree0.2398 2447 7.57 %
Rwork0.2029 --
obs0.2058 32330 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.07 Å2 / Biso mean: 41.1595 Å2 / Biso min: 20.08 Å2
Refinement stepCycle: final / Resolution: 2.1→29.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 4 323 3531
Biso mean--31.53 44.12 -
Num. residues----409
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.14290.31941260.2601171799
2.1429-2.18940.27151450.24851735100
2.1894-2.24040.31241300.26621744100
2.2404-2.29640.32471640.27841725100
2.2964-2.35840.26171390.21941743100
2.3584-2.42780.28141350.2091738100
2.4278-2.50610.24941470.20921725100
2.5061-2.59560.29351560.2141735100
2.5956-2.69950.26391180.21781769100
2.6995-2.82230.24241450.22311771100
2.8223-2.97090.23621540.22231735100
2.9709-3.15690.27461090.22791780100
3.1569-3.40030.24451460.21691754100
3.4003-3.74190.23761420.2017176699
3.7419-4.2820.21291690.17361766100
4.282-5.38970.19371530.15981800100
5.3897-29.7940.20921690.1752188099
Refinement TLS params.Method: refined / Origin x: 35.6944 Å / Origin y: -0.2893 Å / Origin z: 3.7086 Å
111213212223313233
T0.2531 Å2-0.0086 Å2-0.0001 Å2-0.2196 Å2-0.0041 Å2--0.2161 Å2
L1.133 °2-0.0804 °2-0.2731 °2-0.1479 °20.0373 °2--0.2836 °2
S-0.0273 Å °-0.07 Å °-0.0112 Å °0.0416 Å °0.0264 Å °0.0114 Å °0.0129 Å °0.011 Å °0.0001 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 DIFFRACTION1allE3 - 4
5X-RAY DIFFRACTION1allS1 - 337

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