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- PDB-5ip3: Tomato spotted wilt tospovirus nucleocapsid protein-ssDNA complex -

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Basic information

Entry
Database: PDB / ID: 5ip3
TitleTomato spotted wilt tospovirus nucleocapsid protein-ssDNA complex
Components
  • DNA (5'-D(P*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')
  • Nucleoprotein
KeywordsViral protein/DNA / Viral protein / nucleocapsid protein / Bunyavirus / Tospovirus / Viral protein-DNA complex
Function / homologyTospovirus nucleocapsid protein / Tospovirus nucleocapsid protein / viral nucleocapsid / ribonucleoprotein complex / RNA binding / DNA / Nucleoprotein
Function and homology information
Biological speciesTomato spotted wilt virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_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_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_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 2.1Mar 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 2.2Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: DNA (5'-D(P*TP*TP*TP*TP*T)-3')
E: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')
F: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)99,8486
Polymers99,8486
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.940, 86.457, 66.322
Angle α, β, γ (deg.)90.000, 112.100, 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:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resid 2:23 or resid 34:223)B2 - 23
121chain A and (resid 2:23 or resid 34:223)B34 - 223
211chain B and (resid 2:23 or resid 34:223)C2 - 23
221chain B and (resid 2:23 or resid 34:223)C34 - 223
311chain C and (resid 2:23 or resid 34:223)A2 - 23
321chain C and (resid 2:23 or resid 34:223)A34 - 223

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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: DNA chain DNA (5'-D(P*TP*TP*TP*TP*T)-3')


Mass: 1476.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 2084.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')


Mass: 1780.199 Da / Num. of mol.: 1 / 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: 1.83 Å3/Da / Density % sol: 32.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH7.5, 25% (w/v) PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 25, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→47 Å / Num. obs: 14540 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.58 % / Biso Wilson estimate: 99.92 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.08 / Χ2: 0.959 / Net I/σ(I): 17.11 / Num. measured all: 110284
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3-3.180.7880.9282.3817177232022730.99698
3.18-3.40.9290.4874.6516968219821940.52299.8
3.4-3.670.980.2638.1915921206120620.282100
3.67-4.020.9950.12414.9914505188818820.13399.7
4.02-4.490.9970.07822.913093171417090.08499.7
4.49-5.170.9980.0628.3411562153015250.06599.7
5.17-6.310.9980.05830.729583128912880.06299.9
6.31-8.850.9990.04238.937393101910150.04599.6
8.85-47.0350.9990.03845.140816045910.04197.8

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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→37.753 Å / FOM work R set: 0.7153 / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2913 1069 7.36 %Random
Rwork0.2505 13465 --
obs0.2534 14534 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.56 Å2 / Biso mean: 105.19 Å2 / Biso min: 61.17 Å2
Refinement stepCycle: final / Resolution: 3→37.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5666 328 0 0 5994
Num. residues----751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056092
X-RAY DIFFRACTIONf_angle_d0.9388243
X-RAY DIFFRACTIONf_chiral_restr0.039958
X-RAY DIFFRACTIONf_plane_restr0.004978
X-RAY DIFFRACTIONf_dihedral_angle_d16.5252349
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B3028X-RAY DIFFRACTION5.971TORSIONAL
12C3028X-RAY DIFFRACTION5.971TORSIONAL
13A3028X-RAY DIFFRACTION5.971TORSIONAL
LS refinement shellResolution: 3→3.134 Å
RfactorNum. reflection% reflection
Rfree0.3994 145 -
Rwork0.3583 1612 -
obs--98 %
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)
14.19320.5784-0.05060.6730.22893.7167-0.0156-0.0822-0.0710.0111-0.00060.12240.27040.2210.06060.90520.06970.05070.63520.1290.795320.418550.318155.3505
21.05820.80190.77870.68570.96334.9817-0.03030.2169-0.053-0.12220.12980.03190.33220.6643-0.18340.7548-0.00170.04340.7952-0.02350.919417.70948.900425.0566
32.81230.14441.31550.215-0.37064.0504-0.42370.08060.86030.12260.05680.2979-0.2862-0.91470.36670.9760.0154-0.08121.1216-0.06931.3573-5.751761.74640.3072
41.1642-0.19040.94290.4238-0.21620.7685-0.8526-0.9510.22160.36550.43110.3462-0.30850.13870.21341.6629-0.1736-0.12961.26930.20831.168615.455646.554833.5355
53.38310.62040.58046.17722.64457.1474-1.22540.8147-0.1077-1.28441.0912-0.6921-1.03420.35490.02111.78170.0137-0.14640.7055-0.07751.196712.330350.275450.4219
62.69321.30920.14723.18941.30030.65670.00570.70710.24640.59540.9246-0.77140.45330.5647-0.70481.2669-0.21820.05781.4402-0.28541.4856-4.180353.159836.8805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain BB4 - 252
2X-RAY DIFFRACTION2chain CC2 - 257
3X-RAY DIFFRACTION3chain AA3 - 250
4X-RAY DIFFRACTION4chain EE1 - 7
5X-RAY DIFFRACTION5chain DD1 - 5
6X-RAY DIFFRACTION6chain FF1 - 6

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