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- PDB-5ip2: Tomato spotted wilt tospovirus nucleocapsid protein-ssRNA complex -

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Basic information

Entry
Database: PDB / ID: 5ip2
TitleTomato spotted wilt tospovirus nucleocapsid protein-ssRNA complex
Components
  • Nucleoprotein
  • RNA (5'-D(P*UP*UP*U)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsVIRAL PROTEIN/RNA / Viral protein / nucleocapsid protein / Bunyavirus / Tospovirus / VIRAL PROTEIN-RNA complex
Function / homologyTospovirus nucleocapsid protein / Tospovirus nucleocapsid protein / helical viral capsid / viral nucleocapsid / ribonucleoprotein complex / RNA binding / RNA / RNA (> 10) / Nucleoprotein
Function and homology information
Biological speciesTomato spotted wilt virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKomoda, K. / Narita, M. / Yamashita, K. / Tanaka, I. / Yao, M.
CitationJournal: J. Virol. / Year: 2017
Title: Asymmetric Trimeric Ring Structure of the Nucleocapsid Protein of Tospovirus.
Authors: Komoda, K. / Narita, M. / Yamashita, K. / Tanaka, I. / Yao, M.
History
DepositionMar 9, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 2.0Jun 14, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_source / entity_poly / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_symm_contact / struct_conf / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id ..._atom_site.auth_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_strand_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_id
Revision 2.1Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 2.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Nucleoprotein
C: Nucleoprotein
A: Nucleoprotein
E: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
F: RNA (5'-D(P*UP*UP*U)-3')
D: RNA (5'-D(P*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)102,0276
Polymers102,0276
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-124 kcal/mol
Surface area33670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.208, 94.732, 70.917
Angle α, β, γ (deg.)90.000, 112.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B and (resid 2:23 or resid 34:223)
21chain C and (resid 2:23 or resid 34:223)
31chain A and (resid 2:23 or resid 34:223)

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
11SERSERPHEPHEchain A and (resid 2:23 or resid 34:223)BA2 - 2323 - 44
12PHEPHEASNASNchain A and (resid 2:23 or resid 34:223)BA34 - 22355 - 244
21SERSERPHEPHEchain B and (resid 2:23 or resid 34:223)CB2 - 2323 - 44
22PHEPHEASNASNchain B and (resid 2:23 or resid 34:223)CB34 - 22355 - 244
31SERSERPHEPHEchain C and (resid 2:23 or resid 34:223)AC2 - 2323 - 44
32PHEPHEASNASNchain C and (resid 2:23 or resid 34:223)AC34 - 22355 - 244

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein


Mass: 31502.514 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tomato spotted wilt virus / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) pRARE2 / References: UniProt: F4ZD19
#2: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 5772.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-D(P*UP*UP*U)-3')


Mass: 873.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH7.5, 25% (w/v) PEG 1000, 0.1M glycine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.3→38.58 Å / Num. obs: 12585 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 134.64 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.052 / Χ2: 0.982 / Net I/σ(I): 16.51 / Num. measured all: 46942
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.3-3.50.7130.8131.757440203019850.94897.8
3.5-3.740.9050.4093.667261190418980.47699.7
3.74-4.030.9780.1847.66742178317700.21499.3
4.03-4.410.9930.09913.376175162716290.115100
4.41-4.930.9960.063195575149414880.07499.6
4.93-5.670.9980.04525.134872131913110.05399.4
5.67-6.910.9980.03731.384069112411170.04399.4
6.91-9.620.9990.02245.130608918820.02699
9.62-38.5780.9990.0251.7117485355050.02394.4

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Processing

Software
NameVersionClassification
XDSdata processing
PHENIXdev_1426refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YBW

4ybw
PDB Unreleased entry


Resolution: 3.3→38.578 Å / FOM work R set: 0.6635 / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3166 919 7.3 %Random
Rwork0.2823 11662 --
obs0.2847 12581 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 278.71 Å2 / Biso mean: 139.01 Å2 / Biso min: 84.74 Å2
Refinement stepCycle: final / Resolution: 3.3→38.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5439 100 120 0 5659
Biso mean--241.06 --
Num. residues----696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025739
X-RAY DIFFRACTIONf_angle_d0.5317726
X-RAY DIFFRACTIONf_chiral_restr0.02929
X-RAY DIFFRACTIONf_plane_restr0.002919
X-RAY DIFFRACTIONf_dihedral_angle_d10.8042236
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3140X-RAY DIFFRACTION3.593TORSIONAL
12B3140X-RAY DIFFRACTION3.593TORSIONAL
13C3140X-RAY DIFFRACTION3.593TORSIONAL
LS refinement shellResolution: 3.2987→3.4725 Å
RfactorNum. reflection% reflection
Rfree0.422 126 -
Rwork0.3857 1628 -
obs--97 %
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)
11.89070.31340.6653-0.62360.9722.5310.4003-0.5810.31810.233-0.05960.28850.6630.22350.00021.6507-0.04480.13041.2503-0.04581.605314.685249.071357.7466
20.63961.0735-0.4141.45661.1923.72620.09490.3923-0.00220.3222-0.00950.36220.73920.1729-0.02271.0906-0.10920.00061.08690.0491.143815.482248.247225.5709
31.4344-0.52410.33072.43420.57440.9034-0.14660.03970.30340.2909-0.212-0.1762-0.3723-0.3928-0.00011.15760.0546-0.03261.2303-0.09241.4456-8.90164.709440.2867
40.3790.17860.53610.08310.22150.6982-0.7406-0.693-0.11370.7834-0.75610.46130.3366-0.8082-2.0782.3292-2.00261.1662.0920.2821.979811.729248.796533.2027
50.1139-0.0108-0.01610.0002-0.01730.02470.122-0.37180.0826-0.928-0.2780.8034-0.0401-1.18510.00051.73590.0698-1.07051.9269-0.6913.4974-4.77355.73731.809
60.0290.00790.05190.0076-0.0050.0654-1.37380.1448-0.4761-0.7073-0.55120.1768-0.0480.3895-0.00194.4757-0.0170.16841.8349-0.58442.429.54647.97250.277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain BB2 - 248
2X-RAY DIFFRACTION2chain CC2 - 244
3X-RAY DIFFRACTION3chain AA2 - 244
4X-RAY DIFFRACTION4chain EE1 - 5
5X-RAY DIFFRACTION5chain DD1 - 3
6X-RAY DIFFRACTION6chain FF1 - 3

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