[English] 日本語
Yorodumi
- PDB-2zi0: Crystal structure of Tav2b/siRNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zi0
TitleCrystal structure of Tav2b/siRNA complex
Components
  • Protein 2b
  • RNA (5'-D(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*UP*UP*U)-3')
KeywordsGENE REGULATION/RNA / RNAi suppression / Nucleus / Suppressor of RNA silencing / GENE REGULATION-RNA COMPLEX
Function / homology
Function and homology information


host cell nucleus / RNA binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3800 / Cucumovirus protein 2B / Cucumovirus protein 2B / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Suppressor of silencing 2b
Similarity search - Component
Biological speciesTomato aspermy virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.82 Å
AuthorsYuan, Y.A. / Chen, H.-Y.
CitationJournal: Embo Rep. / Year: 2008
Title: Structural basis for RNA-silencing suppression by Tomato aspermy virus protein 2b
Authors: Chen, H.-Y. / Yang, J. / Lin, C. / Yuan, Y.A.
History
DepositionFeb 12, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein 2b
B: Protein 2b
C: RNA (5'-D(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*UP*UP*U)-3')
D: RNA (5'-D(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)31,5864
Polymers31,5864
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-56 kcal/mol
Surface area14370 Å2
MethodPISA
2
A: Protein 2b
B: Protein 2b
C: RNA (5'-D(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*UP*UP*U)-3')
D: RNA (5'-D(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*UP*UP*U)-3')

A: Protein 2b
B: Protein 2b
C: RNA (5'-D(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*UP*UP*U)-3')
D: RNA (5'-D(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)63,1728
Polymers63,1728
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area18380 Å2
ΔGint-149 kcal/mol
Surface area24210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.455, 122.043, 28.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Protein 2b / Tav2b


Mass: 9140.991 Da / Num. of mol.: 2 / Fragment: UNP residues 1-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tomato aspermy virus / Gene: RNA4A / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8UYT3
#2: RNA chain RNA (5'-D(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*UP*UP*U)-3') / siRNA


Mass: 6651.948 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG 1500, 1.0M Ammonium formate, 100mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2Ammonium formate11
3PEG11
4HOH11
5MES12
6Ammonium formate12
7PEG12
8HOH12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9794, 0.9790
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.9791
ReflectionResolution: 2.8→50 Å / Num. all: 7336 / Num. obs: 7336 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rsym value: 0.107 / Net I/σ(I): 20.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 4.44 / Rsym value: 0.488 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.82→49.85 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.844 / SU B: 27.231 / SU ML: 0.265 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 3.944 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27599 353 4.6 %RANDOM
Rwork0.2137 ---
obs0.21648 7336 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.782 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.82→49.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms993 810 0 18 1821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211911
X-RAY DIFFRACTIONr_angle_refined_deg1.5272.4852738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9815113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59322.20359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.1115228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9691518
X-RAY DIFFRACTIONr_chiral_restr0.0730.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021136
X-RAY DIFFRACTIONr_nbd_refined0.1960.2718
X-RAY DIFFRACTIONr_nbtor_refined0.2820.21250
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.340.24
X-RAY DIFFRACTIONr_mcbond_it0.971.5599
X-RAY DIFFRACTIONr_mcangle_it1.3642925
X-RAY DIFFRACTIONr_scbond_it1.14731698
X-RAY DIFFRACTIONr_scangle_it1.9164.51813
LS refinement shellResolution: 2.818→2.891 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 14 -
Rwork0.281 473 -
obs--93.3 %
Refinement TLS params.Method: refined / Origin x: 3.3926 Å / Origin y: -77.5938 Å / Origin z: -11.7571 Å
111213212223313233
T-0.0411 Å20.0074 Å2-0.0114 Å2--0.0703 Å2-0.0216 Å2---0.0589 Å2
L1.428 °2-0.2619 °2-0.4154 °2-1.7047 °2-0.441 °2--1.2975 °2
S-0.1038 Å °-0.1022 Å °0.2437 Å °0.0441 Å °0.0847 Å °-0.1021 Å °-0.2067 Å °0.0717 Å °0.0191 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC7 - 587 - 58
2X-RAY DIFFRACTION1BD7 - 587 - 58
3X-RAY DIFFRACTION1CA1 - 191 - 19
4X-RAY DIFFRACTION1DB1 - 191 - 19

+
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://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