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- PDB-6t6l: Mopeia Virus Exonuclease domain complexed soak with Alendronate -

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Basic information

Entry
Database: PDB / ID: 6t6l
TitleMopeia Virus Exonuclease domain complexed soak with Alendronate
ComponentsNucleoprotein
KeywordsMETAL BINDING PROTEIN / 3-5 Exonuclease / complex
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 / viral nucleocapsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / RNA 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
Similarity search - Domain/homology
Biological speciesMopeia mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.757 Å
AuthorsNguyen, T.H.V. / Ferron, F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Iucrj / Year: 2022
Title: Inhibition of Arenaviridae nucleoprotein exonuclease by bisphosphonate
Authors: Nguyen, T.H.V. / Yekwa, E. / Selisko, B. / Canard, B. / Alvarez, K. / Ferron, F.
History
DepositionOct 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0509
Polymers70,6893
Non-polymers3616
Water14,214789
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6833
Polymers23,5631
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6833
Polymers23,5631
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6833
Polymers23,5631
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.211, 111.337, 49.149
Angle α, β, γ (deg.)90.000, 104.170, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-949-

HOH

21B-867-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 369 through 480 or resid 482 through 516 or resid 518 through 570))
21(chain B and (resid 369 through 480 or resid 482 through 516 or resid 518 through 570))
31(chain C and (resid 369 through 480 or resid 482 through 516 or resid 518 through 570))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERILEILE(chain A and (resid 369 through 480 or resid 482 through 516 or resid 518 through 570))AA369 - 4805 - 116
12LEULEUGLNGLN(chain A and (resid 369 through 480 or resid 482 through 516 or resid 518 through 570))AA482 - 516118 - 152
13LYSLYSLEULEU(chain A and (resid 369 through 480 or resid 482 through 516 or resid 518 through 570))AA518 - 570154 - 206
21SERSERILEILE(chain B and (resid 369 through 480 or resid 482 through 516 or resid 518 through 570))BB369 - 4805 - 116
22LEULEUGLNGLN(chain B and (resid 369 through 480 or resid 482 through 516 or resid 518 through 570))BB482 - 516118 - 152
23LYSLYSLEULEU(chain B and (resid 369 through 480 or resid 482 through 516 or resid 518 through 570))BB518 - 570154 - 206
31SERSERILEILE(chain C and (resid 369 through 480 or resid 482 through 516 or resid 518 through 570))CC369 - 4805 - 116
32LEULEUGLNGLN(chain C and (resid 369 through 480 or resid 482 through 516 or resid 518 through 570))CC482 - 516118 - 152
33LYSLYSLEULEU(chain C and (resid 369 through 480 or resid 482 through 516 or resid 518 through 570))CC518 - 570154 - 206

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 23563.014 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mopeia mammarenavirus / Gene: NP, N / Production host: Escherichia coli (E. coli)
References: UniProt: Q5S581, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES 25-27 % PEG 8000 / PH range: 6.7-7

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 19, 2018 / Details: Silicon sensor
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.757→64.58 Å / Num. obs: 67897 / % possible obs: 98.4 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.046 / Rrim(I) all: 0.089 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.76-1.853.60.4563596799380.8620.2790.5372.698.8
5.56-64.583.50.05740421290.9950.0310.05920.395.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.6 Å64.58 Å
Translation2.6 Å64.58 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.3phasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SX8

6sx8


Resolution: 1.757→47.654 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.47
RfactorNum. reflection% reflection
Rfree0.2221 3470 5.11 %
Rwork0.1914 --
obs0.193 67877 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.17 Å2 / Biso mean: 29.2184 Å2 / Biso min: 11.41 Å2
Refinement stepCycle: final / Resolution: 1.757→47.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4877 0 6 789 5672
Biso mean--20.22 37.11 -
Num. residues----617
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1812X-RAY DIFFRACTION8.29TORSIONAL
12B1812X-RAY DIFFRACTION8.29TORSIONAL
13C1812X-RAY DIFFRACTION8.29TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.757-1.78080.27351190.2405256999
1.7808-1.80620.26611270.238260299
1.8062-1.83320.28471530.23256899
1.8332-1.86180.24671540.2333254498
1.8618-1.89230.29051290.2301260298
1.8923-1.9250.31231300.2232257899
1.925-1.960.23271410.2194259699
1.96-1.99770.27281360.2174255098
1.9977-2.03850.24451400.2176253596
2.0385-2.08280.24621520.2165250098
2.0828-2.13120.24131530.2112260799
2.1312-2.18450.28191410.2126258399
2.1845-2.24360.26961360.2037261599
2.2436-2.30960.251500.1993257099
2.3096-2.38420.24161340.2023257999
2.3842-2.46940.23921430.2016262099
2.4694-2.56820.25261520.1956252998
2.5682-2.68510.22391280.2025253996
2.6851-2.82660.24051440.1972258899
2.8266-3.00370.22961240.202260899
3.0037-3.23560.18841390.1817259599
3.2356-3.56110.19511380.1747258998
3.5611-4.07620.17461370.162255297
4.0762-5.13460.17211710.1523259699
5.1346-47.6540.2415990.1875259395

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