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- PDB-5w0o: Structure of human TUT7 catalytic module (CM) in complex with dsRNA -

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Basic information

Entry
Database: PDB / ID: 5w0o
TitleStructure of human TUT7 catalytic module (CM) in complex with dsRNA
Components
  • Terminal uridylyltransferase 7
  • double-stranded RNARNA
KeywordsTRANSFERASE/RNA / terminal uridyltransferase / TUTase / TRANSFERASE-RNA complex
Function / homology
Function and homology information


polyuridylation-dependent mRNA catabolic process / retrotransposon silencing by mRNA destabilization / uridylyltransferase activity / RNA 3' uridylation / RNA 3'-end processing / RNA uridylyltransferase / RNA uridylyltransferase activity / nuclear-transcribed mRNA poly(A) tail shortening / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA metabolic process ...polyuridylation-dependent mRNA catabolic process / retrotransposon silencing by mRNA destabilization / uridylyltransferase activity / RNA 3' uridylation / RNA 3'-end processing / RNA uridylyltransferase / RNA uridylyltransferase activity / nuclear-transcribed mRNA poly(A) tail shortening / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA metabolic process / Deadenylation of mRNA / pre-miRNA processing / oocyte maturation / miRNA binding / Zygotic genome activation (ZGA) / RNA binding / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger C2H2 type domain signature. / Nucleotidyltransferase superfamily / zinc finger ...Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger C2H2 type domain signature. / Nucleotidyltransferase superfamily / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / RNA / RNA (> 10) / Terminal uridylyltransferase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.488 Å
AuthorsFaehnle, C.R. / Walleshauser, J. / Joshua-Tor, L.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis.
Authors: Faehnle, C.R. / Walleshauser, J. / Joshua-Tor, L.
History
DepositionMay 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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: Terminal uridylyltransferase 7
B: Terminal uridylyltransferase 7
C: double-stranded RNA
D: double-stranded RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0686
Polymers99,0994
Non-polymers9682
Water90150
1
A: Terminal uridylyltransferase 7
C: double-stranded RNA
D: double-stranded RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8184
Polymers54,3343
Non-polymers4841
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-28 kcal/mol
Surface area20690 Å2
MethodPISA
2
B: Terminal uridylyltransferase 7
C: double-stranded RNA
D: double-stranded RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8184
Polymers54,3343
Non-polymers4841
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-31 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.825, 80.851, 181.830
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 Terminal uridylyltransferase 7 / TUT7 / TUTase 7 / Zinc finger CCHC domain-containing protein 6


Mass: 44765.824 Da / Num. of mol.: 2
Fragment: nucleotidyltransferase domain (UNP residues 983-1365)
Mutation: D1160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZCCHC6, HS2, KIAA1711, TUT7 / Plasmid: Multi-Bac, pFL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q5VYS8, RNA uridylyltransferase
#2: RNA chain double-stranded RNA / RNA


Mass: 4783.889 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M trisodium citrate, pH 5.5, 14% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.488→181.832 Å / Num. obs: 35240 / % possible obs: 99.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 61.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.4
Reflection shellResolution: 2.488→2.51 Å / Rmerge(I) obs: 0.734 / CC1/2: 0.733

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
SCALAdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5W0M

5w0m


Resolution: 2.488→45.458 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 1774 5.05 %
Rwork0.2054 33375 -
obs0.2079 35149 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.04 Å2 / Biso mean: 78.5625 Å2 / Biso min: 36.58 Å2
Refinement stepCycle: final / Resolution: 2.488→45.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5337 640 58 50 6085
Biso mean--62.53 61.76 -
Num. residues----685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066236
X-RAY DIFFRACTIONf_angle_d0.98584
X-RAY DIFFRACTIONf_chiral_restr0.049978
X-RAY DIFFRACTIONf_plane_restr0.005961
X-RAY DIFFRACTIONf_dihedral_angle_d14.7273645
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4881-2.55540.31931250.271225292654100
2.5554-2.63060.33711600.267925112671100
2.6306-2.71550.3441410.270325432684100
2.7155-2.81250.32741320.255125282660100
2.8125-2.92510.3461240.257925982722100
2.9251-3.05820.24631220.249325572679100
3.0582-3.21940.30841210.245625842705100
3.2194-3.4210.28411190.227225672686100
3.421-3.6850.2571340.208525882722100
3.685-4.05570.2251630.186225662729100
4.0557-4.6420.22211200.160126062726100
4.642-5.84650.22221690.180926322801100
5.8465-45.46510.24431440.1992566271093
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)
13.93091.6158-2.0883.6757-1.9582.7936-0.00770.67450.21760.0980.08620.3346-0.0906-0.2051-0.07290.3658-0.0903-0.05770.60970.02020.4752-46.365593.69.954
24.26681.0309-2.78983.683-0.68952.625-0.21890.51350.1425-0.29760.09610.0230.03850.02980.15460.2624-0.0439-0.08740.57570.07150.359-36.737294.49067.7353
34.55430.2767-1.90782.74350.56112.6948-0.4920.9291-1.0252-0.14070.03190.20770.7506-0.69590.31270.5775-0.22320.10980.5908-0.18470.736-48.269376.20829.8848
45.27120.0116-3.70242.0874-0.48196.7148-0.25570-1.4648-0.1027-0.2971-0.13220.44210.56060.46540.6146-0.0350.06860.46950.03470.9564-39.570473.422718.3325
57.5408-5.3002-0.49653.78370.8675.464-0.4444-0.90990.62440.68190.417-0.0037-0.9070.09470.18620.9134-0.09190.01520.5367-0.01690.6175-54.026588.832333.4984
62.8431-1.50090.50843.62051.42121.7301-0.0168-0.2371-0.37580.542-0.0830.41920.4354-0.23020.13030.76450.0050.0710.47470.04370.5605-15.03967.485863.6873
74.76971.18521.96426.95271.89216.71-0.00940.96260.3944-0.84410.1047-0.1945-0.0630.5316-0.16530.61420.03190.09910.4930.10860.4871-2.079369.633950.5413
83.20970.16750.41172.73730.04543.16960.0201-0.37270.40130.3944-0.20030.5195-0.4884-0.36880.18870.7280.12440.12320.4683-0.05740.5929-18.79385.000270.3375
97.7244-5.8756-3.00775.4482.82123.78390.86751.04962.6488-1.3524-0.58430.4727-1.577-0.3061-0.40681.27980.1492-0.05830.44820.04421.2456-12.7292100.693559.792
106.56051.73860.13443.46721.34882.413-0.08770.73390.5459-0.3326-0.10950.6696-0.5353-0.37240.15630.6420.2129-0.09540.45980.0030.6905-24.806385.969956.9022
112.2933-0.9644.11370.1482-1.74786.12250.10690.7052-0.05850.1657-0.1230.11920.35070.8324-0.00950.8172-0.0122-0.12191.0070.33350.7666-15.777188.199228.4932
121.5038-0.38353.68511.41-1.83186.88620.1310.825-0.0845-0.5420.0950.21960.08810.6705-0.10190.8590.0307-0.16411.0690.29890.7984-13.365588.187134.3499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 987:1074)A987 - 1074
2X-RAY DIFFRACTION2(chain A and resseq 1075:1153)A1075 - 1153
3X-RAY DIFFRACTION3(chain A and resseq 1154:1248)A1154 - 1248
4X-RAY DIFFRACTION4(chain A and resseq 1249:1318)A1249 - 1318
5X-RAY DIFFRACTION5(chain A and resseq 1319:1336)A1319 - 1336
6X-RAY DIFFRACTION6(chain B and resseq 992:1067)B992 - 1067
7X-RAY DIFFRACTION7(chain B and resseq 1068:1123)B1068 - 1123
8X-RAY DIFFRACTION8(chain B and resseq 1124:1266)B1124 - 1266
9X-RAY DIFFRACTION9(chain B and resseq 1267:1273)B1267 - 1273
10X-RAY DIFFRACTION10(chain B and resseq 1276:1332)B1276 - 1332
11X-RAY DIFFRACTION11(chain C and resseq 1:15)C1 - 15
12X-RAY DIFFRACTION12(chain D and resseq 1:15)D1 - 15

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