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- PDB-5wu2: Crystal structure of human Tut1 bound with BaUTP, form I -

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Basic information

Entry
Database: PDB / ID: 5wu2
TitleCrystal structure of human Tut1 bound with BaUTP, form I
ComponentsSpeckle targeted PIP5K1A-regulated poly(A) polymerase
KeywordsTRANSFERASE / Terminal nucleotidyl transferase
Function / homology
Function and homology information


U6 snRNA 3'-end processing / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / snRNA processing / RNA uridylyltransferase / RNA uridylyltransferase activity / mRNA cleavage and polyadenylation specificity factor complex / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA 3'-end processing / enzyme-substrate adaptor activity ...U6 snRNA 3'-end processing / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / snRNA processing / RNA uridylyltransferase / RNA uridylyltransferase activity / 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 / mitochondrion / RNA binding / nucleoplasm / ATP binding / metal ion binding / cytosol
Similarity search - Function
Star-PAP, RNA recognition motif / TUTase nucleotidyltransferase domain / 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 ...Star-PAP, RNA recognition motif / TUTase nucleotidyltransferase domain / 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
: / URIDINE 5'-TRIPHOSPHATE / Speckle targeted PIP5K1A-regulated poly(A) polymerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.95 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 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,9498
Polymers124,6352
Non-polymers1,3146
Water0
1
A: Speckle targeted PIP5K1A-regulated poly(A) polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9754
Polymers62,3181
Non-polymers6573
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-16 kcal/mol
Surface area23500 Å2
MethodPISA
2
B: Speckle targeted PIP5K1A-regulated poly(A) polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9754
Polymers62,3181
Non-polymers6573
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-16 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.330, 88.400, 184.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 62317.711 Da / Num. of mol.: 2 / Fragment: UNP residues 141-874 / Mutation: C372A, C415A, C501A, C504S
Source method: isolated from a genetically manipulated source
Details: Sequence of 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. C372A, C415A, C501A, and ...Details: Sequence of 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. C372A, C415A, 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
#2: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Hepes pH 7.5, PEG3350, Tacsimate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.5 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 51527 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 28.7 % / Biso Wilson estimate: 58.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.252 / Net I/σ(I): 11.26
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.95-3.022.1021.520.706199.1
3.02-3.11.5422.070.826199.9
3.1-3.191.1722.740.897199.9
3.19-3.290.8733.570.9461100
3.29-3.40.6244.960.968199.9
3.4-3.520.5076.170.981100
3.52-3.650.3967.70.9851100
3.65-3.80.3049.740.9911100
3.8-3.970.25311.310.9941100
3.97-4.170.213.870.996199.9
4.17-4.390.16616.010.9971100
4.39-4.660.14816.920.9981100
4.66-4.980.14118.320.9981100
4.98-5.380.15417.290.9981100
5.38-5.890.16615.670.9971100
5.89-6.590.14917.660.9981100
6.59-7.610.11720.870.9991100
7.61-9.310.06432.370.9991100
9.31-13.170.04743.0311100
13.170.04546.531198.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.95→19.938 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36
RfactorNum. reflection% reflection
Rfree0.2938 2572 5.01 %
Rwork0.246 --
obs0.2484 51334 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 181.06 Å2 / Biso mean: 68.65 Å2 / Biso min: 10.38 Å2
Refinement stepCycle: final / Resolution: 2.95→19.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7522 0 62 0 7584
Biso mean--40.09 --
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037748
X-RAY DIFFRACTIONf_angle_d0.87210540
X-RAY DIFFRACTIONf_chiral_restr0.0291188
X-RAY DIFFRACTIONf_plane_restr0.0041366
X-RAY DIFFRACTIONf_dihedral_angle_d13.8462866
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9454-3.00190.35751420.36722664280699
3.0019-3.06290.35421430.345127212864100
3.0629-3.12930.46541370.342226982835100
3.1293-3.20180.37211420.333627022844100
3.2018-3.28150.41241390.317427352874100
3.2815-3.36990.38251450.295527282873100
3.3699-3.46850.32671440.275426912835100
3.4685-3.57990.32561460.288626992845100
3.5799-3.7070.27521420.263527442886100
3.707-3.85440.29451420.239527042846100
3.8544-4.02850.28791470.252327252872100
4.0285-4.23890.23791410.227626902831100
4.2389-4.50170.27831440.224827072851100
4.5017-4.84460.28951470.218127352882100
4.8446-5.32370.30831440.206927012845100
5.3237-6.07490.22471390.231627162855100
6.0749-7.58310.28281430.219727002843100
7.5831-19.93870.21541450.16622702284799
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)
11.6968-0.23-0.89411.5566-0.22833.8753-0.0944-0.26570.0734-0.02080.13420.0111-0.0605-0.0201-0.03960.27150.0399-0.02910.2326-0.08240.3576157.9163197.8765197.7154
23.19110.85570.55071.79310.63891.75080.0492-0.8139-0.6511-0.2302-0.04010.2316-0.3378-0.45060.08170.42420.0227-0.04320.84580.11610.4344122.1096199.8252215.5581
31.6772-0.35270.44221.1547-0.72913.2219-0.0809-0.0391-0.0929-0.03140.07960.07760.23110.1066-0.00290.28260.02770.00780.225-0.10450.3085175.7551155.6767197.6575
41.89240.26130.19790.9531-0.472.0867-0.1193-1.27340.45360.3850.2123-0.32480.23050.3511-0.04890.41160.1413-0.1060.9106-0.30740.6602211.4804153.6766215.6329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 145:599)A145 - 599
2X-RAY DIFFRACTION2(chain A and resid 600:877)A600 - 877
3X-RAY DIFFRACTION3(chain B and resid 145:599)B145 - 599
4X-RAY DIFFRACTION4(chain B and resid 600:877)B600 - 877

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