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- PDB-5wu6: Crystal structure of apo human Tut1, form IV -

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Basic information

Entry
Database: PDB / ID: 5wu6
TitleCrystal structure of apo human Tut1, form IV
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 / RRM (RNA recognition motif) domain / Zinc finger C2H2 superfamily / Nucleotidyltransferase superfamily / Zinc finger C2H2-type / RNA recognition motif ...Star-PAP, RNA recognition motif / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Zinc-finger of C2H2 type / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
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: 3.209 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 / 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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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
C: Speckle targeted PIP5K1A-regulated poly(A) polymerase
D: Speckle targeted PIP5K1A-regulated poly(A) polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,48511
Polymers211,3154
Non-polymers1707
Water0
1
A: Speckle targeted PIP5K1A-regulated poly(A) polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8773
Polymers52,8291
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Speckle targeted PIP5K1A-regulated poly(A) polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8773
Polymers52,8291
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Speckle targeted PIP5K1A-regulated poly(A) polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8773
Polymers52,8291
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Speckle targeted PIP5K1A-regulated poly(A) polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8532
Polymers52,8291
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.530, 142.530, 282.690
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: 52828.816 Da / Num. of mol.: 4 / Fragment: UNP residues 54-599 / Mutation: C372A, C399A, C415A, C501A, C504A, 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
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg

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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: 3.4 Å3/Da / Density % sol: 68.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Tris pH 7.0, PEG3350, MgCl2.

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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: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 48397 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 26.4 % / Biso Wilson estimate: 70.09 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.375 / Net I/σ(I): 14.32
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
3.21-3.292.3451.880.677198.9
3.29-3.381.7872.490.766199.9
3.38-3.481.5263.070.8291100
3.48-3.591.1324.120.8991100
3.59-3.710.8885.450.9491100
3.71-3.840.7056.730.9691100
3.84-3.980.5518.530.9781100
3.98-4.140.44410.310.9821100
4.14-4.330.35512.720.9891100
4.33-4.540.30114.730.9921100
4.54-4.780.24517.60.9961100
4.78-5.070.22718.720.9961100
5.07-5.420.23817.620.9951100
5.42-5.860.24217.490.9951100
5.86-6.420.21519.70.9961100
6.42-7.180.16225.030.997199.9
7.18-8.290.10434.460.9991100
8.29-10.150.05458.0711100
10.15-14.350.04567.5311100
14.350.0557.421196.7

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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: 5WU1

5wu1


Resolution: 3.209→19.993 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.55
RfactorNum. reflection% reflection
Rfree0.2418 2408 5 %
Rwork0.2024 --
obs0.2043 48155 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 223.09 Å2 / Biso mean: 73.73 Å2 / Biso min: 28.4 Å2
Refinement stepCycle: final / Resolution: 3.209→19.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12187 0 7 0 12194
Biso mean--54.25 --
Num. residues----1589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312434
X-RAY DIFFRACTIONf_angle_d0.7716870
X-RAY DIFFRACTIONf_chiral_restr0.0261899
X-RAY DIFFRACTIONf_plane_restr0.0042223
X-RAY DIFFRACTIONf_dihedral_angle_d12.5624575
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2091-3.27440.3051360.30582594273099
3.2744-3.34520.31931390.289926442783100
3.3452-3.42270.30621390.275226422781100
3.4227-3.50780.31511410.274526622803100
3.5078-3.60210.29251390.246426542793100
3.6021-3.70750.27121400.238826582798100
3.7075-3.82630.30841400.229926562796100
3.8263-3.96210.2611410.213826792820100
3.9621-4.11940.24131400.197726532793100
4.1194-4.30510.20331410.181126962837100
4.3051-4.52960.22991410.175326702811100
4.5296-4.80970.20071420.167726982840100
4.8097-5.17510.2071430.17627062849100
5.1751-5.6850.26381430.182427222865100
5.685-6.48290.2471440.197727472891100
6.4829-8.07720.22821460.194727662912100
8.0772-19.99290.17531530.158329003053100
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)
18.5973.28421.96235.33411.86442.3571-0.34070.44630.5459-0.2869-0.1478-0.6949-0.47361.20090.51450.84050.141-0.0810.71690.09340.6291-113.887640.693266.6276
22.6596-0.0811-0.65350.7673-0.3512.8005-0.06190.1293-0.0289-0.0593-0.0475-0.0967-0.2119-0.05020.14660.50640.08420.08730.33260.07090.3772-95.95817.109547.941
38.38674.00795.17023.26060.36498.190.21630.0372-0.7080.7396-0.07140.17372.01580.1807-0.07890.96610.10210.23350.6975-0.19410.7631-108.976555.69242.6938
40.5278-0.41330.42712.7664-0.42351.93230.0527-0.03020.01550.19010.04480.0933-0.6903-0.0568-0.09130.8521-0.07210.14640.38320.04180.3871-69.902934.71423.6015
56.33150.9545-0.8266.255-3.69452.33750.05510.5529-0.5783-0.6521-0.35650.44150.7093-1.90710.23980.5048-0.26960.0551.1885-0.19810.6048-16.3769-50.273664.2415
62.849-0.74340.8460.6845-0.34192.1448-0.1073-0.2869-0.0474-0.01690.0793-0.03690.00220.46590.03430.42880.0625-0.02320.6649-0.06350.3649-31.6426-11.723550.2292
70.6505-0.46890.40653.04620.30921.9045-0.0761-0.07920.06390.19820.0276-0.12480.1371-0.17480.05430.3461-0.0416-0.08270.38050.01290.3561-57.5501-31.873318.3474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 55:126)A55 - 126
2X-RAY DIFFRACTION2(chain A and resid 145:597)A145 - 597
3X-RAY DIFFRACTION3(chain B and resid 55:125)B55 - 125
4X-RAY DIFFRACTION4(chain B and resid 145:597)B145 - 597
5X-RAY DIFFRACTION5(chain C and resid 55:126)C55 - 126
6X-RAY DIFFRACTION6(chain C and resid 145:597)C145 - 597
7X-RAY DIFFRACTION7(chain D and resid 145:597)D145 - 597

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