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- PDB-7v39: Crystal structure of NP exonuclease-PCMB complex -

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Basic information

Entry
Database: PDB / ID: 7v39
TitleCrystal structure of NP exonuclease-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 / virus-mediated perturbation of host defense response / RNA binding / identical protein binding / metal ion 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: 2.2 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)56,1966
Polymers55,3872
Non-polymers8084
Water4,918273
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0983
Polymers27,6941
Non-polymers4042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11180 Å2
MethodPISA
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0983
Polymers27,6941
Non-polymers4042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-0 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.185, 76.292, 140.784
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 27693.641 Da / Num. of mol.: 2
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-HGB / 4-(HYDROXYMERCURY)BENZOIC ACID


Mass: 338.711 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6HgO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M DL-Malic acid pH 7.0, 20% w/v Polyethylene glycol 3,350, 2mM Sodium p-hydroxymercuribenzoate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 28303 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 29.98 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.038 / Rrim(I) all: 0.097 / Χ2: 1.941 / Net I/σ(I): 11.8 / Num. measured all: 179251
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.286.10.39527930.9090.1730.4321.185100
2.28-2.376.10.33627670.9330.1460.3671.218100
2.37-2.486.20.2927810.9510.1250.3161.295100
2.48-2.616.30.22527820.9690.0960.2451.376100
2.61-2.776.40.17628130.9830.0750.1921.492100
2.77-2.996.50.14227970.9890.060.1551.812100
2.99-3.296.50.128270.9950.0420.1082.259100
3.29-3.766.60.06728300.9970.0280.0722.34299.9
3.76-4.736.40.05728800.9970.0240.0622.94199.7
4.73-306.20.05330330.9980.0230.0583.24999.8

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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: 2.2→28.816 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.87
RfactorNum. reflection% reflection
Rfree0.2298 2097 7.44 %
Rwork0.1995 --
obs0.2018 28191 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 236.39 Å2 / Biso mean: 38.577 Å2 / Biso min: 14.99 Å2
Refinement stepCycle: final / Resolution: 2.2→28.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 22 273 3494
Biso mean--94.72 41.93 -
Num. residues----409
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2-2.25120.28171340.2261707
2.2512-2.30740.26921550.22181694
2.3074-2.36980.2721490.22011695
2.3698-2.43950.27921360.22251709
2.4395-2.51820.27111330.21611735
2.5182-2.60810.24661270.22071718
2.6081-2.71250.26761380.22441722
2.7125-2.83580.27641340.21931719
2.8358-2.98520.2411510.22351725
2.9852-3.1720.21341460.22221734
3.172-3.41660.22031240.19781748
3.4166-3.75970.17561340.18271747
3.7597-4.30220.21531590.17691751
4.3022-5.41450.21331320.17291800
5.4145-28.8160.22371450.19251890
Refinement TLS params.Method: refined / Origin x: -36.9261 Å / Origin y: 6.3774 Å / Origin z: -35.6693 Å
111213212223313233
T0.1647 Å2-0.0095 Å20.0439 Å2-0.1435 Å20.0089 Å2--0.1943 Å2
L0.9429 °2-0.0571 °20.6959 °2-0.6346 °2-0.0275 °2--1.3494 °2
S-0.1021 Å °0.0598 Å °0.073 Å °-0.0216 Å °0.0216 Å °0.0037 Å °-0.0668 Å °0.0218 Å °0.0652 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA363 - 569
2X-RAY DIFFRACTION1allB361 - 569
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 280
5X-RAY DIFFRACTION1allD1 - 2

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