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- PDB-4gv3: Structures of Lassa and Tacaribe viral nucleoproteins with or wit... -

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Basic information

Entry
Database: PDB / ID: 4gv3
TitleStructures of Lassa and Tacaribe viral nucleoproteins with or without 5 triphosphate dsRNA substrate reveal a unique 3 -5 exoribonuclease mechanism to suppress type I interferon production
Components
  • Nucleoprotein
  • RNA (5'-R(*(GTP)P*GP*GP*C)-3')
  • RNA (5'-R(P*CP*GP*CP*CP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / DDEDH family / 3'-5'exoribonuclease / RNA BINDING PROTEIN-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 / 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
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
: / RNA / Nucleoprotein
Similarity search - Component
Biological speciesLassa virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.68 Å
AuthorsJiang, X. / Huang, Q. / Wang, W. / Dong, H. / Ly, H. / Liang, Y. / Dong, C.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structures of Arenaviral Nucleoproteins with Triphosphate dsRNA Reveal a Unique Mechanism of Immune Suppression.
Authors: Jiang, X. / Huang, Q. / Wang, W. / Dong, H. / Ly, H. / Liang, Y. / Dong, C.
History
DepositionAug 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Feb 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_asym_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.pdbx_leaving_atom_flag / _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
B: RNA (5'-R(*(GTP)P*GP*GP*C)-3')
C: RNA (5'-R(P*CP*GP*CP*CP*C)-3')
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1685
Polymers27,0473
Non-polymers1202
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-18 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.580, 46.580, 208.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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RNA chain , 2 types, 2 molecules BC

#1: RNA chain RNA (5'-R(*(GTP)P*GP*GP*C)-3')


Mass: 1455.801 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(P*CP*GP*CP*CP*C)-3')


Mass: 1520.976 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#3: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 24070.678 Da / Num. of mol.: 1 / Fragment: UNP residues 364-569
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus / Strain: josiah / Gene: N / Plasmid: Plou3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: P13699

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Non-polymers , 3 types, 179 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 18.5% PEGMME 5000, 0.1M sodium citrate pH4.5 and 2.4% PEGMME350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2011
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.68→52.24 Å / Num. obs: 25994 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.065 / Net I/σ(I): 9.1
Reflection shellResolution: 1.68→1.77 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.449 / % possible all: 96.1

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Processing

Software
NameVersionClassification
DNAdata collection
PHASESphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementResolution: 1.68→52.21 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.807 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1374 5 %RANDOM
Rwork0.199 ---
obs0.2 25994 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å20 Å20 Å2
2---1.69 Å20 Å2
3---3.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.064 Å0.021 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.68→52.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 181 2 177 1988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0191865
X-RAY DIFFRACTIONr_bond_other_d0.0010.021674
X-RAY DIFFRACTIONr_angle_refined_deg1.0161.9212560
X-RAY DIFFRACTIONr_angle_other_deg0.75733874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1335206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81324.53375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78415298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8681510
X-RAY DIFFRACTIONr_chiral_restr0.0590.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211956
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr1.10833539
X-RAY DIFFRACTIONr_sphericity_free21.219573
X-RAY DIFFRACTIONr_sphericity_bonded4.35153614
LS refinement shellResolution: 1.68→1.73 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 89 -
Rwork0.184 1889 -
obs--99.9 %

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