[English] 日本語
Yorodumi
- PDB-5ip2: Tomato spotted wilt tospovirus nucleocapsid protein-ssRNA complex -

+
Open data


ID or keywords:

Loading...

-
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more