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- PDB-4fvu: Structural basis for the dsRNA specificity of the Lassa virus NP ... -

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Basic information

Entry
Database: PDB / ID: 4fvu
TitleStructural basis for the dsRNA specificity of the Lassa virus NP exonuclease
Components
  • Nucleoprotein
  • RNA (5'-R(*CP*UP*CP*CP*CP*UP*CP*C)-3')
  • RNA (5'-R(*GP*GP*AP*GP*GP*GP*AP*G)-3')
KeywordsHYDROLASE/RNA / arenavirus / nucleoprotein / dsRNA / exonuclease / HYDROLASE / HYDROLASE-RNA 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 / 3'-5' exonuclease activity / 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 / viral nucleocapsid / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / identical protein binding / metal ion binding
Similarity search - Function
Arenaviral nucleoprotein, C-terminal domain / 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 / Nucleotidyltransferase; domain 5 / WD40 repeat / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLassa virus Josiah
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsHastie, K.M. / King, L.B. / Zandonatti, M.A. / Saphire, E.O.
CitationJournal: Plos One / Year: 2012
Title: Structural Basis for the dsRNA Specificity of the Lassa Virus NP Exonuclease.
Authors: Hastie, K.M. / King, L.B. / Zandonatti, M.A. / Saphire, E.O.
History
DepositionJun 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.3Jun 20, 2018Group: Data collection / Category: diffrn_radiation
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_scattering_type
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: RNA (5'-R(*GP*GP*AP*GP*GP*GP*AP*G)-3')
C: RNA (5'-R(*CP*UP*CP*CP*CP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3855
Polymers32,2953
Non-polymers902
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-25 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.772, 84.311, 79.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nucleoprotein / / Nucleocapsid protein / Protein N


Mass: 27212.068 Da / Num. of mol.: 1 / Mutation: E391A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus Josiah / Strain: Mouse/Sierra Leone/Josiah/1976 / Gene: N / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: P13699

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RNA chain , 2 types, 2 molecules BC

#2: RNA chain RNA (5'-R(*GP*GP*AP*GP*GP*GP*AP*G)-3')


Mass: 2684.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA synthesized by IDT DNA / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: RNA chain RNA (5'-R(*CP*UP*CP*CP*CP*UP*CP*C)-3')


Mass: 2398.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA synthesized by IDT DNA / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 6 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 0.2 M MgCl2 hexahydrate and 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2011
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.9→39.904 Å

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→39.904 Å / SU ML: 0.92 / σ(F): 0 / Phase error: 30.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 334 4.75 %
Rwork0.197 --
obs0.1996 7030 99.74 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.611 Å2 / ksol: 0.293 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--26.3252 Å20 Å2-0 Å2
2--47.7901 Å20 Å2
3----21.4649 Å2
Refinement stepCycle: LAST / Resolution: 2.91→39.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1560 336 2 4 1902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141985
X-RAY DIFFRACTIONf_angle_d1.332742
X-RAY DIFFRACTIONf_dihedral_angle_d14.837752
X-RAY DIFFRACTIONf_chiral_restr0.094332
X-RAY DIFFRACTIONf_plane_restr0.005296
LS refinement shellResolution: 2.9102→3.6661 Å
RfactorNum. reflection% reflection
Rfree0.3626 170 -
Rwork0.2371 3263 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 5.542 Å / Origin y: -19.5742 Å / Origin z: -21.2741 Å
111213212223313233
T0.4536 Å20.0633 Å20.017 Å2-0.5337 Å2-0.0342 Å2--0.4738 Å2
L2.8511 °2-0.2197 °20.8938 °2-1.7933 °20.1077 °2--2.2557 °2
S-0.0602 Å °-0.1345 Å °-0.0828 Å °0.1929 Å °0.0076 Å °0.1411 Å °-0.0884 Å °-0.2129 Å °0.0624 Å °
Refinement TLS groupSelection details: all

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