[English] 日本語
Yorodumi
- PDB-6bjh: CIRV p19 mutant T111S in complex with siRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bjh
TitleCIRV p19 mutant T111S in complex with siRNA
Components
  • RNA (5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP*UP*U)-3')
  • RNA (5'-R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3')
  • RNA silencing suppressor p19
KeywordsRNA BINDING PROTEIN / Viral suppressor / RNA silencing siRNA / high affinity for human miRNA-122
Function / homology
Function and homology information


virion component / virus-mediated perturbation of host defense response / RNA binding
Similarity search - Function
RNA silencing suppressor P19 / Tombusvirus p19 core protein / Tombusvirus P19 superfamily / Tombusvirus P19 core protein / Enolase-like; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA silencing suppressor p19
Similarity search - Component
Biological speciesCarnation Italian ringspot virus
Lampyridae (fireflies)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsFoss, D.V. / Schirle, N.T. / MacRae, I.J. / Pezacki, J.P.
Citation
Journal: Febs Open Bio / Year: 2019
Title: Structural insights into interactions between viral suppressor of RNA silencing protein p19 mutants and small RNAs.
Authors: Foss, D.V. / Schirle, N.T. / MacRae, I.J. / Pezacki, J.P.
#1: Journal: Biochemistry / Year: 2011
Title: Enhanced specificity of the viral suppressor of RNA silencing protein p19 toward sequestering of human microRNA-122.
Authors: Cheng, J. / Danielson, D.C. / Nasheri, N. / Singaravelu, R. / Pezacki, J.P.
History
DepositionNov 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA silencing suppressor p19
B: RNA silencing suppressor p19
C: RNA (5'-R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3')
D: RNA (5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)52,0464
Polymers52,0464
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-53 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.788, 46.219, 54.181
Angle α, β, γ (deg.)109.850, 112.110, 95.520
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein RNA silencing suppressor p19 / 19 kDa symptom severity modulator


Mass: 19344.348 Da / Num. of mol.: 2 / Mutation: T111S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carnation Italian ringspot virus / Gene: ORF4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q66104
#2: RNA chain RNA (5'-R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3')


Mass: 6666.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lampyridae (fireflies)
#3: RNA chain RNA (5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP*UP*U)-3')


Mass: 6690.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lampyridae (fireflies)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 3-12% PEG 1500, 100 mM Sodium Acetate pH 4.6, 10-40 mM MgCl2

-
Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.58→34.25 Å / Num. obs: 10184 / % possible obs: 85.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 28.13 Å2 / CC1/2: 0.961 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.075 / Rrim(I) all: 0.107 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.58-2.71.80.25110520.4620.2510.35572.5
8.95-34.2520.0252480.9960.0250.03585.5

-
Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIX(1.10.1_2155)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RPU

1rpu


Resolution: 2.58→34.037 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 28.08
RfactorNum. reflection% reflection
Rfree0.278 469 5.12 %
Rwork0.2241 --
obs0.227 9153 77.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.03 Å2 / Biso mean: 32.5888 Å2 / Biso min: 1.33 Å2
Refinement stepCycle: final / Resolution: 2.58→34.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 890 0 129 3300
Biso mean---28.21 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023323
X-RAY DIFFRACTIONf_angle_d0.4294687
X-RAY DIFFRACTIONf_chiral_restr0.03530
X-RAY DIFFRACTIONf_plane_restr0.002455
X-RAY DIFFRACTIONf_dihedral_angle_d8.7421858
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5729-2.94510.35861430.29312717286073
2.9451-3.70970.32581460.22442876302276
3.7097-34.04030.22631800.19943091327182
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)
12.4606-0.70411.16253.3137-1.22593.56560.2795-0.1572-0.1520.18250.29840.47250.4482-0.446-0.24560.32070.01470.0420.28380.07990.15622.477149.761376.3665
21.67381.21840.81681.18740.45790.78-0.1005-0.21290.77270.01360.13070.5954-0.488-0.0246-0.00450.92550.17460.12110.463-0.18350.97439.72572.528470.9958
31.3433-0.3218-0.20961.2431-0.49791.47820.1017-0.21530.08120.329-0.1151-0.1151-0.04640.17170.11110.2249-0.03940.0570.1620.1070.08113.851551.552575.1993
40.93230.1496-0.00442.0635-0.97461.49060.0006-0.2422-0.2340.1904-0.1812-0.19830.04990.26250.10860.2518-0.07130.05330.1920.11740.134417.409247.606466.7314
50.16660.01210.27390.0010.01960.4524-0.0040.21110.135-0.1851-0.0019-0.0358-0.1225-0.03950.15260.3954-0.03580.05420.31830.14780.165722.170950.97738.9036
61.6632-0.10210.85080.07490.23991.67790.1227-0.2395-0.34630.11980.17880.14730.3834-0.06680.39240.2819-0.09170.05470.24860.13020.160823.160140.230547.6355
71.7779-0.76250.91811.1999-0.07091.1971-0.0371-0.093-0.2981-0.02690.047-0.0861-0.07980.14080.02670.1466-0.0864-0.09440.26380.04630.333431.487651.993849.8376
80.7220.165-0.24230.20960.3921.2417-0.02170.0290.13190.03020.06620.0302-0.2366-0.17520.0860.13620.0291-0.0710.10160.08260.23717.940755.896653.8378
93.386-0.45811.11781.33230.42060.84560.1148-0.5036-0.13280.32460.0054-0.32730.06410.0098-0.0330.2656-0.1865-0.07020.47490.04510.196627.354352.872660.0597
105.7967-5.80932.81179.2448-0.04623.60780.0337-0.3478-0.7319-0.0351-0.44210.19980.19610.36440.25340.29060.00510.00770.31830.15870.327712.05138.98542.9517
110.6158-0.5737-0.71844.7018-1.8022.3043-0.13650.3704-0.00920.0290.23550.54750.038-0.4058-0.02150.19050.0295-0.04230.23050.00360.45333.924151.71156.081
122.96321.20712.01394.354.07564.17390.6796-0.28540.70431.091-0.40580.8944-1.0697-2.1556-0.19130.82440.11420.41120.68390.1180.8342-6.971467.316462.9078
136.26032.8264-4.79329.5615-4.6324.89880.11530.725-0.5949-0.33570.1740.0120.7204-0.4455-0.29250.3855-0.0056-0.10.2562-0.12590.6511-2.001559.96165.6328
144.0312-1.17292.97653.5355-0.62462.21610.4110.5877-0.4506-0.4726-0.42820.76860.1059-1.1006-0.02320.33440.0689-0.13440.6276-0.05620.37273.222955.247350.2084
151.3830.79541.97480.54351.00893.0054-0.07660.4678-0.4709-0.0690.0428-0.30460.5461-0.0352-0.15660.4846-0.0209-0.07150.3465-0.23640.557710.235334.797746.9169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 38 )A7 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 57 )A39 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 101 )A58 - 101
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 147 )A102 - 147
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 38 )B8 - 38
6X-RAY DIFFRACTION6chain 'B' and (resid 39 through 74 )B39 - 74
7X-RAY DIFFRACTION7chain 'B' and (resid 75 through 101 )B75 - 101
8X-RAY DIFFRACTION8chain 'B' and (resid 102 through 129 )B102 - 129
9X-RAY DIFFRACTION9chain 'B' and (resid 130 through 149 )B130 - 149
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 5 )C1 - 5
11X-RAY DIFFRACTION11chain 'C' and (resid 6 through 15 )C6 - 15
12X-RAY DIFFRACTION12chain 'C' and (resid 16 through 19 )C16 - 19
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 5 )D1 - 5
14X-RAY DIFFRACTION14chain 'D' and (resid 6 through 10 )D6 - 10
15X-RAY DIFFRACTION15chain 'D' and (resid 11 through 20 )D11 - 20

+
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