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- PDB-5wu3: Crystal structure of human Tut1 bound with MgUTP, form II -

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Basic information

Entry
Database: PDB / ID: 5wu3
TitleCrystal structure of human Tut1 bound with MgUTP, form II
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 / MOLECULAR REPLACEMENT / Resolution: 2.703 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _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)125,71910
Polymers124,5072
Non-polymers1,2128
Water362
1
A: Speckle targeted PIP5K1A-regulated poly(A) polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8605
Polymers62,2541
Non-polymers6064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area23760 Å2
MethodPISA
2
B: Speckle targeted PIP5K1A-regulated poly(A) polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8605
Polymers62,2541
Non-polymers6064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.794, 85.115, 93.760
Angle α, β, γ (deg.)90.000, 99.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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: 62253.586 Da / Num. of mol.: 2 / Fragment: UNP residues 235-304, 651-750 / Mutation: C372A, C399A, C415A, C501A, C504S, C574A
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, C399A, C415A, C501A, ...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, C399A, C415A, C501A, C504S, and C574A 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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Non-polymers , 5 types, 10 molecules

#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
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: 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: 2.7→50 Å / Num. obs: 33809 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 52.87 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.27
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.7-2.770.761.750.602197
2.77-2.850.552.40.748199.7
2.85-2.930.4552.90.82199.9
2.93-3.020.3633.50.853199.6
3.02-3.120.3084.020.901199.4
3.12-3.230.2365.240.945199.7
3.23-3.350.1757.110.968199.5
3.35-3.490.1458.850.977199.3
3.49-3.650.10811.220.988199.4
3.65-3.820.08113.580.992198.4
3.82-4.030.07115.990.994197.8
4.03-4.270.0520.910.997199.9
4.27-4.570.044230.997199.6
4.57-4.940.03824.50.997199.6
4.94-5.410.0424.010.997199.3
5.41-6.040.04224.350.997199.5
6.04-6.980.03925.880.998199.4
6.98-8.550.02930.030.998199.2
8.55-12.090.02836.680.998198.5
12.090.02834.820.998195.6

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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: 2.703→19.926 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.29
RfactorNum. reflection% reflection
Rfree0.2569 1685 5 %
Rwork0.2288 --
obs0.2302 33721 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 260.59 Å2 / Biso mean: 68.11 Å2 / Biso min: 22.3 Å2
Refinement stepCycle: final / Resolution: 2.703→19.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7527 0 70 2 7599
Biso mean--72.04 38.19 -
Num. residues----969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057759
X-RAY DIFFRACTIONf_angle_d0.99810552
X-RAY DIFFRACTIONf_chiral_restr0.0341189
X-RAY DIFFRACTIONf_plane_restr0.0041368
X-RAY DIFFRACTIONf_dihedral_angle_d14.3942858
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.703-2.78230.39181360.34782592272897
2.7823-2.87180.33981420.310426912833100
2.8718-2.97420.36521390.301526402779100
2.9742-3.09280.30021410.311726842825100
3.0928-3.2330.38771410.29326812822100
3.233-3.40270.28481400.260826492789100
3.4027-3.61470.2771410.24782687282899
3.6147-3.89190.26151380.22442627276598
3.8919-4.280.21691400.20712661280199
4.28-4.89130.21831420.184726972839100
4.8913-6.13260.26521420.204726952837100
6.1326-19.92680.1771430.17442732287599
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)
12.09910.2891-0.62911.683-1.05853.7627-0.07650.03640.0441-0.00390.15160.00590.04450.0087-0.06130.2789-0.0005-0.03340.2653-0.03630.2829-10.4699-11.9888-13.8246
25.66240.3688-0.81844.9268-0.22384.1486-0.01221.2512-0.6435-0.5007-0.0048-0.5221-0.11691.04490.01980.5314-0.00740.02741.005-0.12220.486825.5912-11.531-31.3594
32.2418-0.61610.76561.8596-1.19963.6596-0.0804-0.1207-0.11650.16080.18360.0512-0.0423-0.0316-0.08280.2674-0.0050.00180.2622-0.03830.3771-50.365-10.991213.6902
45.31840.2673-0.37623.972-0.57044.62250.1855-1.04330.56710.4254-0.2981-0.42960.33641.2010.11850.59490.0209-0.0510.9587-0.0660.3977-14.2604-11.299431.1726
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 599:877)A599 - 877
3X-RAY DIFFRACTION3(chain B and resid 145:598)B145 - 598
4X-RAY DIFFRACTION4(chain B and resid 599:877)B599 - 877

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