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- PDB-5wu5: Crystal structure of apo human Tut1, form III -

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Basic information

Entry
Database: PDB / ID: 5wu5
TitleCrystal structure of apo human Tut1, form III
ComponentsSpeckle targeted PIP5K1A-regulated poly(A) polymerase
KeywordsTRANSFERASE / Terminal nucleotidyl transferase
Function / homology
Function and homology information


U6 snRNA 3'-end processing / RNA uridylyltransferase / regulation of RNA metabolic process / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / RNA 3'-end processing / RNA uridylyltransferase activity / snRNA processing / mRNA cleavage and polyadenylation specificity factor complex / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity ...U6 snRNA 3'-end processing / RNA uridylyltransferase / regulation of RNA metabolic process / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / RNA 3'-end processing / RNA uridylyltransferase activity / snRNA processing / mRNA cleavage and polyadenylation specificity factor complex / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA 3'-end processing / enzyme-substrate adaptor activity / U6 snRNA binding / mRNA 3'-UTR binding / nuclear speck / nucleolus / enzyme binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Star-PAP, RNA recognition motif / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Zinc-finger of C2H2 type / Nucleotidyltransferase superfamily / Zinc finger C2H2 superfamily / Zinc finger C2H2-type ...Star-PAP, RNA recognition motif / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Zinc-finger of C2H2 type / Nucleotidyltransferase superfamily / Zinc finger C2H2 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
Speckle targeted PIP5K1A-regulated poly(A) polymerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.404 Å
AuthorsYamashita, S. / Tomita, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS26251009 Japan
CitationJournal: Nat Commun / Year: 2017
Title: Crystal structures of U6 snRNA-specific terminal uridylyltransferase
Authors: Yamashita, S. / Takagi, Y. / Nagaike, T. / Tomita, K.
History
DepositionDec 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 8, 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: Speckle targeted PIP5K1A-regulated poly(A) polymerase
B: Speckle targeted PIP5K1A-regulated poly(A) polymerase
C: Speckle targeted PIP5K1A-regulated poly(A) polymerase
D: Speckle targeted PIP5K1A-regulated poly(A) polymerase


Theoretical massNumber of molelcules
Total (without water)249,5274
Polymers249,5274
Non-polymers00
Water00
1
A: Speckle targeted PIP5K1A-regulated poly(A) polymerase


Theoretical massNumber of molelcules
Total (without water)62,3821
Polymers62,3821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Speckle targeted PIP5K1A-regulated poly(A) polymerase


Theoretical massNumber of molelcules
Total (without water)62,3821
Polymers62,3821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Speckle targeted PIP5K1A-regulated poly(A) polymerase


Theoretical massNumber of molelcules
Total (without water)62,3821
Polymers62,3821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Speckle targeted PIP5K1A-regulated poly(A) polymerase


Theoretical massNumber of molelcules
Total (without water)62,3821
Polymers62,3821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-41 kcal/mol
Surface area87180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.140, 173.140, 208.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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: 62381.836 Da / Num. of mol.: 4 / Fragment: UNP residues 141-874 / Mutation: C501A, C504S
Source method: isolated from a genetically manipulated source
Details: 141-874(C-term) of human Tut1 was cloned to pET22b vector with NdeI and XhoI sites. Residues of 235-304 and 651-750 were deleted for crystallization. C501A and C504S mutations were ...Details: 141-874(C-term) of human Tut1 was cloned to pET22b vector with NdeI and XhoI sites. Residues of 235-304 and 651-750 were deleted for crystallization. C501A and C504S mutations were introduced to improve the crystals.
Source: (gene. exp.) Homo sapiens (human) / Gene: TUT1, RBM21 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H6E5, polynucleotide adenylyltransferase, RNA uridylyltransferase

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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: 3.13 Å3/Da / Density % sol: 66.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Sodium Cacodylate pH 7.0, PEG4000, Tacsimate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 39562 / % possible obs: 89.8 % / Observed criterion σ(I): -3 / Redundancy: 13 % / Biso Wilson estimate: 54.46 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.334 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
3.4-3.491.2812.320.711132.1
3.49-3.591.3832.330.759157.4
3.59-3.690.9893.240.777175.6
3.69-3.811.0872.960.826192.3
3.81-3.930.9593.370.8951100
3.93-4.070.7744.130.924199.9
4.07-4.220.6055.060.944199.9
4.22-4.390.4826.260.9641100
4.39-4.590.3867.870.9761100
4.59-4.810.3348.980.979199.9
4.81-5.070.3259.020.9811100
5.07-5.380.39.340.9841100
5.38-5.750.3178.740.9781100
5.75-6.210.3069.30.9811100
6.21-6.810.24111.320.9881100
6.81-7.610.17514.340.9931100
7.61-8.790.09720.990.996199.9
8.79-10.760.06629.040.9981100
10.76-15.220.05930.280.9991100
15.220.05928.290.998195.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WU2

5wu2


Resolution: 3.404→19.989 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.54
RfactorNum. reflection% reflection
Rfree0.2582 1974 5.02 %
Rwork0.214 --
obs0.2162 39296 89.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 202.31 Å2 / Biso mean: 58.91 Å2 / Biso min: 14.61 Å2
Refinement stepCycle: final / Resolution: 3.404→19.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15026 0 0 0 15026
Num. residues----1936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315354
X-RAY DIFFRACTIONf_angle_d0.83920859
X-RAY DIFFRACTIONf_chiral_restr0.0322351
X-RAY DIFFRACTIONf_plane_restr0.0042730
X-RAY DIFFRACTIONf_dihedral_angle_d12.1755677
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4039-3.48860.3667590.312491497332
3.4886-3.58240.404810.28941651173257
3.5824-3.68720.34981290.28012176230575
3.6872-3.80540.32071540.262673282792
3.8054-3.94040.31141350.244529643099100
3.9404-4.09690.24271630.232229173080100
4.0969-4.28160.24331600.217529443104100
4.2816-4.50490.2561350.202929623097100
4.5049-4.78360.27821520.193329693121100
4.7836-5.14710.20581570.18629603117100
5.1471-5.65440.25271720.197229843156100
5.6544-6.44840.25881500.219830223172100
6.4484-8.03560.22051670.210430293196100
8.0356-19.98950.19721600.162631573317100
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)
13.3434-0.66440.07421.1421-0.55550.8683-0.06460.4712-0.1041-0.23110.0198-0.02730.0448-0.2685-0.02440.4021-0.03480.04980.1008-0.1080.166611.8835-14.1728-26.6789
22.9934-0.4561-0.70394.4032-0.25422.9219-0.0995-0.4077-0.47650.30420.01610.3596-0.07920.07760.06440.3210.09880.06790.16710.02180.4061-4.3703-25.74027.878
32.89910.8773-0.66253.2087-0.47810.50740.0994-0.64280.17030.4039-0.0419-0.3306-0.01850.1793-0.07780.29530.09410.020.2759-0.06070.212529.9395-6.48927.8506
42.5706-0.5795-0.22994.1787-0.51831.54320.1470.3426-0.4881-0.4634-0.0115-0.33450.22580.0664-0.0280.390.0110.2540.0201-0.07470.518951.0971-11.9551-24.9412
50.6968-0.5101-0.20412.58321.06752.2035-0.09120.1735-0.22730.058-0.14350.61690.0378-0.55720.14790.3043-0.00740.11420.20370.0290.409613.4917-66.9738-7.5253
62.1383-0.1685-0.054.1374-0.27192.3786-0.05290.29680.3709-0.5215-0.0147-0.0402-0.51190.06450.02650.61910.09590.07980.02280.0990.259241.7915-60.917-35.2941
71.4159-1.24060.2962.5446-1.07262.14630.0478-0.50210.2050.3680.109-0.536-0.38030.51270.13240.4410.0652-0.11430.0837-0.06110.455256.5927-54.7461-4.6131
83.0861-0.1804-0.11043.04530.19242.83130.0348-0.75640.07931.2501-0.03510.127-0.0167-0.3953-0.00110.93780.21370.08710.54540.06510.342728.4549-60.608722.8951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 145:598)A145 - 598
2X-RAY DIFFRACTION2(chain A and resid 599:876)A599 - 876
3X-RAY DIFFRACTION3(chain B and resid 145:598)B145 - 598
4X-RAY DIFFRACTION4(chain B and resid 599:876)B599 - 876
5X-RAY DIFFRACTION5(chain C and resid 145:598)C145 - 598
6X-RAY DIFFRACTION6(chain C and resid 599:876)C599 - 876
7X-RAY DIFFRACTION7(chain D and resid 145:598)D145 - 598
8X-RAY DIFFRACTION8(chain D and resid 599:876)D599 - 876

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