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- PDB-4gve: Tacaribe nucleoprotein structure -

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Basic information

Entry
Database: PDB / ID: 4gve
TitleTacaribe nucleoprotein structure
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / DEDDH family enzyme
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 / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / virus-mediated perturbation of host defense response ...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 / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / virus-mediated perturbation of host defense response / RNA 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesTacaribe virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0533
Polymers23,9641
Non-polymers902
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.170, 115.170, 56.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 23963.504 Da / Num. of mol.: 1 / Fragment: C-terminal domain residues 364-570
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tacaribe virus / Strain: ATCC strain 11573, Franze-Fernandez / Gene: N, nucleoprotein / Plasmid: Plou3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: P18140
#2: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.94 Å3/Da / Density % sol: 68.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 32% PEG3350, 0.1 M MOPS (pH7.0), and 0.11 M ammonium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2011
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.65
11K, H, -L20.35
ReflectionResolution: 1.73→57.58 Å / Num. all: 39591 / Num. obs: 39191 / % possible obs: 99 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1.9 / Redundancy: 5.8 % / Rmerge(I) obs: 0.084 / Rsym value: 0.083 / Net I/σ(I): 1.9
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.76 / % possible all: 100

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Processing

Software
NameVersionClassification
EDNAdata collection
PHASESphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GV3

4gv3


Resolution: 1.73→57.59 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 5.231 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16686 1896 4.8 %RANDOM
Rwork0.15324 ---
obs0.15389 37294 99.76 %-
all-39391 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.03 Å2
Baniso -1Baniso -2Baniso -3
1--10.16 Å2-0 Å2-0 Å2
2---10.16 Å2-0 Å2
3---20.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.05 Å0.035 Å
Luzzati d res low-4 Å
Luzzati sigma a0.4 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.73→57.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1565 0 2 131 1698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9742175
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5535195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18924.93273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34415282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.803156
X-RAY DIFFRACTIONr_chiral_restr0.090.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221216
X-RAY DIFFRACTIONr_gen_planes_other
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 147 -
Rwork0.252 2662 -
obs--98.05 %
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)
11.53650.95130.73141.82580.6010.9979-0.01470.078-0.0842-0.00210.1203-0.1148-0.07450.1344-0.10560.1757-0.03130.01760.1918-0.01590.078920.583315.92522.6379
21.32650.65160.54361.52590.65380.7649-0.06450.02280.03650.00960.07790.0017-0.11870.105-0.01340.1988-0.03790.02820.18870.00920.065819.798218.22613.3792
31.9360.33591.14491.8687-0.2511.31660.01390.1911-0.0231-0.16570.0921-0.1024-0.11420.3333-0.1060.2138-0.09150.08650.2133-0.00430.115620.673920.9338-3.7385
41.96320.9431-0.05352.3735-0.80573.9041-0.05650.33090.0242-0.01240.22720.1476-0.13330.1302-0.17070.159-0.03330.01090.1999-0.01750.220218.950922.0759-4.2843
53.9840.58190.11350.4244-0.02730.6353-0.06770.5544-0.14470.0757-0.12330.12440.14970.05810.1910.2612-0.02430.1480.2381-0.06380.182121.255422.4875-0.1397
63.00913.813-0.67638.62550.77090.8681-0.0751-0.5836-0.4976-0.2371-0.055-0.483-0.03370.32140.130.3528-0.1544-0.01831.07760.20210.168121.92878.14850.8526
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A358 - 564
2X-RAY DIFFRACTION2A701 - 771
3X-RAY DIFFRACTION3A772 - 805
4X-RAY DIFFRACTION4A806 - 815
5X-RAY DIFFRACTION5A816 - 823
6X-RAY DIFFRACTION6A824 - 829

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