[English] 日本語
Yorodumi
- PDB-5z4a: Structure of Tailor in complex with AGU RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z4a
TitleStructure of Tailor in complex with AGU RNA
Components
  • RNA (5'-R(*AP*GP*U)-3')
  • Terminal uridylyltransferase Tailor
KeywordsTRANSFERASE/RNA / Terminal uridylyltransferase / TRANSFERASE-RNA complex
Function / homology
Function and homology information


positive regulation of miRNA catabolic process / negative regulation of pre-miRNA processing / RNA uridylyltransferase / RNA uridylyltransferase activity / regulatory ncRNA-mediated gene silencing / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
RNA / Terminal uridylyltransferase Tailor
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.637 Å
AuthorsCheng, L. / Li, F. / Jiang, Y. / Yu, H. / Xie, C. / Shi, Y. / Gong, Q.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural insights into a unique preference for 3' terminal guanine of mirtron in Drosophila TUTase tailor.
Authors: Cheng, L. / Li, F. / Jiang, Y. / Yu, H. / Xie, C. / Shi, Y. / Gong, Q.
History
DepositionJan 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 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
B: RNA (5'-R(*AP*GP*U)-3')
A: Terminal uridylyltransferase Tailor


Theoretical massNumber of molelcules
Total (without water)41,3262
Polymers41,3262
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-7 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.717, 84.944, 148.262
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-765-

HOH

-
Components

#1: RNA chain RNA (5'-R(*AP*GP*U)-3')


Mass: 935.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#2: Protein Terminal uridylyltransferase Tailor / TUTase Tailor


Mass: 40390.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Tailor, CG1091 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VI58, RNA uridylyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 47.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium chloride, 0.1M Tris pH 8.4, 15% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.637→50 Å / Num. obs: 48194 / % possible obs: 99.5 % / Redundancy: 12.8 % / Biso Wilson estimate: 19.75 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.025 / Rrim(I) all: 0.089 / Χ2: 0.601 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.86-1.8910.80.49314420.9480.1490.5150.46393.1
1.89-1.9311.30.48916070.9480.1450.5110.46997.3
1.93-1.9611.70.43115640.9730.1270.4490.4898.7
1.96-212.10.37816100.9740.1110.3940.48299.9
2-2.0512.50.31815930.9790.0930.3320.49100
2.05-2.0912.70.2916060.9870.0840.3030.499100
2.09-2.1512.20.25616180.9880.0760.2670.497100
2.15-2.2112.70.21916080.990.0640.2280.508100
2.21-2.2713.60.19716180.9930.0550.2050.541100
2.27-2.3413.80.17216050.9940.0480.1790.538100
2.34-2.4313.60.15415950.9950.0430.160.56100
2.43-2.5213.70.13816360.9950.0390.1440.562100
2.52-2.6413.40.12116170.9970.0340.1260.597100
2.64-2.7812.60.10316220.9970.030.1080.643100
2.78-2.9513.20.0916340.9980.0260.0940.66999.9
2.95-3.1813.90.08116260.9980.0220.0840.697100
3.18-3.513.60.07116560.9980.020.0730.754100
3.5-4.0112.70.06216610.9980.0180.0650.835100
4.01-5.0513.20.05716560.9980.0160.0590.822100
5.05-5012.30.05517710.9990.0160.0570.79100

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.10_2155: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NKT

4nkt


Resolution: 1.637→49.93 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.93
RfactorNum. reflection% reflection
Rfree0.1905 2419 5.02 %
Rwork0.1571 --
obs0.1587 48194 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 168.58 Å2 / Biso mean: 32.491 Å2 / Biso min: 11.77 Å2
Refinement stepCycle: final / Resolution: 1.637→49.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 62 0 243 3134
Biso mean---32.88 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093016
X-RAY DIFFRACTIONf_angle_d0.9794109
X-RAY DIFFRACTIONf_chiral_restr0.059463
X-RAY DIFFRACTIONf_plane_restr0.007516
X-RAY DIFFRACTIONf_dihedral_angle_d14.4161822
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6372-1.67060.21061250.19892547267296
1.6706-1.7070.24751540.191426582812100
1.707-1.74670.22541550.184826762831100
1.7467-1.79030.20831400.179826342774100
1.7903-1.83880.20561310.171226792810100
1.8388-1.89290.21781520.175826762828100
1.8929-1.9540.20451350.167326932828100
1.954-2.02380.18661280.162127112839100
2.0238-2.10480.19531300.160326902820100
2.1048-2.20060.1891540.159126632817100
2.2006-2.31660.17661480.156326822830100
2.3166-2.46180.17641430.151326882831100
2.4618-2.65190.18981630.158126952858100
2.6519-2.91870.20151370.157127432880100
2.9187-3.3410.1951430.159627012844100
3.341-4.20890.18121470.140327602907100
4.2089-49.95290.17511340.149928793013100
Refinement TLS params.Method: refined / Origin x: -3.9806 Å / Origin y: -25.4418 Å / Origin z: 15.7645 Å
111213212223313233
T0.135 Å2-0.0462 Å2-0.0136 Å2-0.1528 Å2-0.0027 Å2--0.1095 Å2
L1.194 °2-0.0622 °20.0946 °2-0.6168 °2-0.4657 °2--1.5044 °2
S-0.0012 Å °0.1029 Å °0.0023 Å °0.0042 Å °0.0109 Å °0.0202 Å °0.0453 Å °0.0595 Å °-0.005 Å °
Refinement TLS groupSelection details: all

+
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