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- PDB-8idf: Crystal structure of human TUT1 complexed with U6 snRNA -

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Basic information

Entry
Database: PDB / ID: 8idf
TitleCrystal structure of human TUT1 complexed with U6 snRNA
Components
  • RNA (53-MER)
  • Speckle targeted PIP5K1A-regulated poly(A) polymerase
KeywordsTRANSFERASE/RNA / nucleotidyl transferase / TRANSFERASE / TRANSFERASE-RNA complex
Function / homology
Function and homology information


U6 snRNA 3'-end processing / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / RNA uridylyltransferase / snRNA processing / RNA uridylyltransferase activity / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / enzyme-substrate adaptor activity ...U6 snRNA 3'-end processing / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / RNA uridylyltransferase / snRNA processing / RNA uridylyltransferase activity / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / enzyme-substrate adaptor activity / : / U6 snRNA binding / mRNA 3'-UTR binding / nuclear speck / nucleolus / enzyme binding / mitochondrion / RNA binding / nucleoplasm / ATP binding / metal ion binding / cytosol
Similarity search - Function
Star-PAP, RNA recognition motif / PAP/25A-associated / Cid1 family poly A polymerase / Zinc-finger of C2H2 type / Zinc finger C2H2 superfamily / Nucleotidyltransferase superfamily / Zinc finger C2H2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...Star-PAP, RNA recognition motif / PAP/25A-associated / Cid1 family poly A polymerase / Zinc-finger of C2H2 type / Zinc finger C2H2 superfamily / Nucleotidyltransferase superfamily / Zinc finger C2H2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Speckle targeted PIP5K1A-regulated poly(A) polymerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsYamashita, S. / Tomita, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H03980 Japan
Japan Society for the Promotion of Science (JSPS)19K16053 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Mechanism of U6 snRNA oligouridylation by human TUT1.
Authors: Yamashita, S. / Tomita, K.
History
DepositionFeb 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Speckle targeted PIP5K1A-regulated poly(A) polymerase
B: RNA (53-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5173
Polymers75,4512
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-45 kcal/mol
Surface area30990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.724, 78.724, 370.272
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Speckle targeted PIP5K1A-regulated poly(A) polymerase / Star-PAP / RNA-binding motif protein 21 / RNA-binding protein 21 / U6 snRNA-specific terminal ...Star-PAP / RNA-binding motif protein 21 / RNA-binding protein 21 / U6 snRNA-specific terminal uridylyltransferase 1 / U6-TUTase


Mass: 58441.289 Da / Num. of mol.: 1
Mutation: deletion 235-304, C19S,C372A,C415A,C501A,C504S,C399A,C574A,D218A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUT1, RBM21 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H6E5, polynucleotide adenylyltransferase, RNA uridylyltransferase
#2: RNA chain RNA (53-MER)


Mass: 17010.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100mM BisTris pH 6.4, 18% PEG 3350, 2% Tacsimate pH 6.0, 8% Acetonitrile

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.27 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27 Å / Relative weight: 1
ReflectionResolution: 3.7→19.99 Å / Num. obs: 13674 / % possible obs: 99.4 % / Redundancy: 42.175 % / Biso Wilson estimate: 110.219 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.532 / Rrim(I) all: 0.538 / Χ2: 0.648 / Net I/σ(I): 8.99 / Num. measured all: 576696 / Scaling rejects: 121
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.7-3.7942.8214.4011.484175010489750.7534.45393
3.79-3.942.9133.4451.98420559809800.8383.486100
3.9-4.0142.1742.8662.66404879609600.9152.9100
4.01-4.1341.0192.093.55387639469450.9512.11699.9
4.13-4.2738.7371.9233.7342828858850.9551.948100
4.27-4.4241.231.5044.69365308868860.9911.523100
4.42-4.5944.3151.3215.47375798488480.991.336100
4.59-4.7744.3011.0527.29353087977970.9931.064100
4.77-4.9943.641.0886.92348687997990.9841.101100
4.99-5.2343.460.9567.92329437587580.9860.967100
5.23-5.5142.7110.8618.13295136926910.990.87199.9
5.51-5.8541.8820.8738.1276006596590.980.883100
5.85-6.2538.8310.6949.52250076446440.9880.703100
6.25-6.7541.4540.51412.1243755885880.9940.521100
6.75-7.3945.1420.38815.63241515355350.9970.393100
7.39-8.2744.2490.21923.02215054864860.9970.222100
8.27-9.5542.8910.13830.56189154414410.9980.14100
9.55-11.6939.9340.11632.98144963633630.9990.118100
11.69-16.5339.3060.09734.06111632852840.9990.09899.6
16.53-19.9936.040.09935.9154061571500.9970.10195.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5wu1

5wu1


Resolution: 3.7→19.99 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3386 680 5.01 %
Rwork0.3047 12892 -
obs0.3063 13572 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 925.09 Å2 / Biso mean: 209.2323 Å2 / Biso min: 39.09 Å2
Refinement stepCycle: final / Resolution: 3.7→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3529 1128 1 0 4658
Biso mean--170.1 --
Num. residues----512
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.7-3.980.37621350.37862538267397
3.98-4.380.37031390.334226002739100
4.38-50.43911390.323725612700100
5-6.270.34341380.354225782716100
6.27-19.990.26791290.242926152744100
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)
16.2787-1.10892.73944.8315-4.05814.66341.3983-0.3102-2.12191.74371.43081.9191-0.0576-1.3549-1.91891.3396-0.3269-0.18881.97830.5691.462139.536-1.012-22.34
26.90050.1407-2.55614.16293.15387.54520.74660.5340.70340.80080.88660.1148-1.8666-1.0647-0.7290.7295-0.2370.02651.34610.41631.23125.39611.673-47.643
31.912-1.6315-0.18874.0051-5.320210.04880.5641-0.5621-0.1430.6492-0.25080.07232.47190.8439-0.19141.25530.16220.17050.4893-0.05410.64486.618-19.144-18.812
46.73134.16382.35074.37-0.03413.51340.5096-1.04351.22571.8857-1.2833-2.7152-1.5426-0.2580.36241.2250.0580.30842.29820.0371.244723.5615.596-38.575
55.98753.75745.49221.63442.99243.97540.4364-2.6664-2.08530.99520.9828-2.11510.0953-0.7619-2.22674.19610.5416-1.24313.2333-0.02623.262242.479-15.618-7.872
60.5601-0.2327-1.17020.09630.48152.4559-0.29890.67922.1781.3253-1.5344-5.4558-0.10780.61930.60534.91850.8329-0.061-0.12680.66212.270612.149-19.402-26.178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:56 OR RESID 1001:1001 ) )A7 - 56
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:56 OR RESID 1001:1001 ) )A1001
3X-RAY DIFFRACTION2( CHAIN A AND RESID 57:134 )A57 - 134
4X-RAY DIFFRACTION3( CHAIN A AND RESID 145:599 )A145 - 599
5X-RAY DIFFRACTION4( CHAIN B AND RESID 1:9 )B1 - 9
6X-RAY DIFFRACTION5( CHAIN B AND RESID 10:51 )B10 - 51
7X-RAY DIFFRACTION6( CHAIN B AND RESID 52:53 )B52 - 53

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