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- PDB-7v38: Crystal structure of NP exonuclease-PCMPS complex -

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Basic information

Entry
Database: PDB / ID: 7v38
TitleCrystal structure of NP exonuclease-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: 2.403 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)56,2346
Polymers55,3872
Non-polymers8464
Water61334
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1173
Polymers27,6941
Non-polymers4232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11310 Å2
MethodPISA
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1173
Polymers27,6941
Non-polymers4232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint0 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.227, 74.012, 140.807
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: 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-PMB / PARA-MERCURY-BENZENESULFONIC ACID


Mass: 357.757 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5HgO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium malonate pH 6.0, 20% 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: 0.99311 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99311 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 20856 / % possible obs: 98.9 % / Redundancy: 11.8 % / Biso Wilson estimate: 48.08 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.025 / Rrim(I) all: 0.089 / Χ2: 1.719 / Net I/σ(I): 10.8 / Num. measured all: 245203
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4910.20.49619040.9460.1520.520.56292.5
2.49-2.59110.40820080.9670.1240.4280.57598.4
2.59-2.711.70.34220770.9760.1020.3570.65999.3
2.7-2.85120.25220640.9910.0750.2630.75299.6
2.85-3.0212.10.20120790.9940.0590.210.923100
3.02-3.2612.10.12620930.9980.0370.1311.414100
3.26-3.5812.40.09921090.9980.0290.1031.98499.9
3.58-4.112.50.07721050.9990.0230.082.67599.7
4.1-5.1612.10.06321510.9990.0190.0663.1599.9
5.16-3011.30.04922660.9990.0150.0523.89699.5

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Processing

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

4g9z


Resolution: 2.403→29.793 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.12
RfactorNum. reflection% reflection
Rfree0.2622 1634 7.86 %
Rwork0.2127 --
obs0.2167 20782 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 206.91 Å2 / Biso mean: 64.0597 Å2 / Biso min: 26.27 Å2
Refinement stepCycle: final / Resolution: 2.403→29.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 24 34 3278
Biso mean--122.78 52.54 -
Num. residues----410
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4032-2.47380.36461310.2955134486
2.4738-2.55370.38061270.2805155998
2.5537-2.64490.37381310.2842159899
2.6449-2.75070.34671220.28171582100
2.7507-2.87580.35761270.2653160799
2.8758-3.02730.29951260.27181595100
3.0273-3.21670.34821390.25111614100
3.2167-3.46470.29361470.23021611100
3.4647-3.81280.27111270.19481625100
3.8128-4.3630.23221440.17431631100
4.363-5.49130.21510.17291646100
5.4913-29.7930.21091620.19331736100
Refinement TLS params.Method: refined / Origin x: 64.0319 Å / Origin y: 67.2699 Å / Origin z: 36.6732 Å
111213212223313233
T0.3487 Å2-0.0053 Å2-0.0592 Å2-0.3474 Å20.0083 Å2--0.2483 Å2
L0.9168 °20.0722 °2-0.7317 °2-0.8002 °2-0.0903 °2--2.6502 °2
S-0.0892 Å °0.0233 Å °-0.012 Å °0.0638 Å °0.0208 Å °-0.0003 Å °0.148 Å °-0.1435 Å °0.078 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 - 2
5X-RAY DIFFRACTION1allS1 - 42

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