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- PDB-5z4j: Structure of Tailor in complex with U4 RNA -

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Basic information

Entry
Database: PDB / ID: 5z4j
TitleStructure of Tailor in complex with U4 RNA
Components
  • RNA (5'-R(*UP*UP*UP*U)-3')
  • Terminal uridylyltransferase Tailor
KeywordsTRANSFERASE/RNA / Terminal uridylyltransferase / TRANSFERASE-RNA complex
Function / homology
Function and homology information


negative regulation of pre-miRNA processing / positive regulation of miRNA catabolic process / 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: 1.82 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 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terminal uridylyltransferase Tailor
B: RNA (5'-R(*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)42,8822
Polymers42,8822
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-15 kcal/mol
Surface area15960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.633, 84.840, 148.307
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-711-

HOH

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Components

#1: Protein Terminal uridylyltransferase Tailor / TUTase Tailor


Mass: 41702.457 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
#2: RNA chain RNA (5'-R(*UP*UP*UP*U)-3')


Mass: 1179.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.59 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 35229 / % possible obs: 99.6 % / Redundancy: 13.1 % / Biso Wilson estimate: 25.17 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.024 / Rrim(I) all: 0.087 / Χ2: 1.122 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.82-1.8513.40.47817170.9830.1340.4970.51199.7
1.85-1.8913.70.4317330.9850.1190.4460.5499.6
1.89-1.9213.60.36217400.9890.1010.3760.5799.7
1.92-1.9613.60.31117290.9910.0870.3230.59499.7
1.96-213.40.26517510.9930.0750.2760.62299.9
2-2.0513.20.22317340.9920.0630.2320.799.8
2.05-2.113.10.19917670.9930.0560.2070.7399.8
2.1-2.1612.20.17717290.9930.0520.1840.80299.6
2.16-2.2212.60.16117560.9930.0470.1680.92899.3
2.22-2.2913.80.14217570.9960.0390.1470.944100
2.29-2.3713.60.12717650.9950.0360.1321.00899.9
2.37-2.4713.60.11517360.9960.0320.1191.09499.6
2.47-2.5813.40.11117670.9960.0310.1151.183100
2.58-2.72130.09617650.9960.0280.11.34399.9
2.72-2.8912.30.08617520.9960.0250.091.57798.5
2.89-3.1113.70.07917860.9980.0220.0821.682100
3.11-3.4313.40.07217760.9980.020.0751.9599.9
3.43-3.9212.60.06417840.9970.0190.0672.1399.7
3.92-4.9412.40.05717830.9980.0170.0592.01898
4.94-5012.10.0519020.9980.0150.0531.58898.9

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Processing

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

4nkt


Resolution: 1.82→37.077 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.77
RfactorNum. reflection% reflection
Rfree0.192 1745 4.97 %
Rwork0.1552 --
obs0.1571 35132 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 267.59 Å2 / Biso mean: 39.9293 Å2 / Biso min: 14.24 Å2
Refinement stepCycle: final / Resolution: 1.82→37.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 77 0 193 3069
Biso mean---36.17 -
Num. residues----353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012960
X-RAY DIFFRACTIONf_angle_d1.0294029
X-RAY DIFFRACTIONf_chiral_restr0.061461
X-RAY DIFFRACTIONf_plane_restr0.007499
X-RAY DIFFRACTIONf_dihedral_angle_d16.0151784
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8167-1.87020.25631320.19472688282097
1.8702-1.93060.20071190.175627782897100
1.9306-1.99960.23671360.174127552891100
1.9996-2.07960.21691430.16827852928100
2.0796-2.17420.21231620.16252746290899
2.1742-2.28890.19861490.162927732922100
2.2889-2.43220.20981360.162627842920100
2.4322-2.620.21851620.162328012963100
2.62-2.88360.21291520.15842764291699
2.8836-3.30060.21341390.161628332972100
3.3006-4.15750.17171510.13552807295899
4.1575-37.08450.15481640.14642873303797
Refinement TLS params.Method: refined / Origin x: 4.1896 Å / Origin y: 25.6082 Å / Origin z: 16.0823 Å
111213212223313233
T0.1705 Å2-0.0468 Å20.0137 Å2-0.1507 Å20.0081 Å2--0.1346 Å2
L1.3514 °2-0.0052 °2-0.0139 °2-0.8001 °20.627 °2--1.7727 °2
S0.008 Å °0.0823 Å °-0.0109 Å °0.0244 Å °-0.0028 Å °-0.0291 Å °-0.0548 Å °-0.0636 Å °0.0019 Å °
Refinement TLS groupSelection details: all

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