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- PDB-4gv6: Structures of Lassa and Tacaribe viral nucleoproteins with or wit... -

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Basic information

Entry
Database: PDB / ID: 4gv6
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 / DEDDH family enzyme / 3'-5' exonuclease / 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 / 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
: / RNA / Nucleoprotein
Similarity search - Component
Biological speciesLassa virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.98 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
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-18 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.510, 46.510, 208.650
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 364-570
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, 150 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 / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 18.5% PEG MME 5000, 0.1 M sodium citrate, and 2.4% PEG MME350, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 176 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 6, 2011
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.98→69.54 Å / Num. obs: 16160 / % possible obs: 89.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 9.8 / Redundancy: 2.2 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.06 / Net I/σ(I): 8
Reflection shellResolution: 1.98→2.08 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.178 / % possible all: 92.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASESphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementResolution: 1.98→52.16 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.262 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 863 5.1 %RANDOM
Rwork0.188 ---
obs0.19 16160 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.65 Å2
Baniso -1Baniso -2Baniso -3
1-18.57 Å20 Å20 Å2
2--18.57 Å20 Å2
3----37.13 Å2
Refinement stepCycle: LAST / Resolution: 1.98→52.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 181 2 148 1959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191865
X-RAY DIFFRACTIONr_bond_other_d0.0010.021674
X-RAY DIFFRACTIONr_angle_refined_deg1.0011.9212560
X-RAY DIFFRACTIONr_angle_other_deg0.79633874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9135206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55324.53375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4315298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7191510
X-RAY DIFFRACTIONr_chiral_restr0.0570.2289
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_restr2.45333539
X-RAY DIFFRACTIONr_sphericity_free30.506562
X-RAY DIFFRACTIONr_sphericity_bonded12.44153585
LS refinement shellResolution: 1.98→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 66 -
Rwork0.189 1164 -
obs--99.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.38020.47310.33230.66140.73521.9092-0.08840.00460.1408-0.1776-0.03870.1251-0.331-0.2210.12720.15380.0415-0.04150.1610.0370.4232-5.77749.09680.7876
21.1081-3.418-0.775910.61362.41670.55190.13880.0582-0.1181-0.5012-0.16830.2139-0.1309-0.04030.02950.23470.0330.02610.1480.02640.4195-0.123115.5334-2.0373
30.11330.0011-0.05390.14740.05580.10080.01160.03030.0132-0.0201-0.0190.0031-0.0372-0.01910.00740.11170.00920.00060.14150.00150.3853-0.24719.736918.2023
40000000000000000.1145-0.0159-0.02930.1381-0.0390.4369-3.3967.45319.5856
50000000000000000.1185-0.0107-0.00330.16080.00860.4141-6.201114.371218.8891
60.05340.0737-0.00740.1162-0.02590.08740.0148-0.00710.0167-0.0176-0.01560.0053-0.00170.00360.00080.12350.01780.00260.1482-0.0010.453-1.75938.683817.9634
70.01210.009-0.00120.0108-0.00040.00020.0363-0.01570.00590.0195-0.0352-0.0203-0.0054-0.0024-0.00110.14390.0231-0.00030.1999-0.01010.4673-3.095510.133114.2695
80.11240.048-0.22580.52810.38861.04060.0587-0.06290.0136-0.1072-0.15560.0095-0.0787-0.03540.09690.1828-0.02090.02210.0910.03990.5420.387311.368912.945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B8 - 11
2X-RAY DIFFRACTION2C2 - 5
3X-RAY DIFFRACTION3A356 - 569
4X-RAY DIFFRACTION4B101
5X-RAY DIFFRACTION5A601
6X-RAY DIFFRACTION6A702 - 801
7X-RAY DIFFRACTION7A802 - 834
8X-RAY DIFFRACTION8A835 - 836

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