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- PDB-5w0b: Structure of human TUT7 catalytic module (CM) -

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Basic information

Entry
Database: PDB / ID: 5w0b
TitleStructure of human TUT7 catalytic module (CM)
ComponentsTerminal uridylyltransferase 7
KeywordsTRANSFERASE / terminal uridyltransferase / TUTase
Function / homology
Function and homology information


polyuridylation-dependent mRNA catabolic process / uridylyltransferase activity / transposable element silencing by mRNA destabilization / RNA uridylyltransferase / RNA 3'-end processing / RNA uridylyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA metabolic process / Deadenylation of mRNA / pre-miRNA processing ...polyuridylation-dependent mRNA catabolic process / uridylyltransferase activity / transposable element silencing by mRNA destabilization / RNA uridylyltransferase / RNA 3'-end processing / RNA uridylyltransferase activity / 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 / cytoplasm / cytosol
Similarity search - Function
Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Nucleotidyltransferase superfamily ...Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Nucleotidyltransferase superfamily / Zinc finger C2H2 type domain signature. / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
IODIDE ION / Terminal uridylyltransferase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.614 Å
AuthorsFaehnle, C.R. / Walleshauser, J. / Joshua-Tor, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114147 United States
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 30, 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 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Terminal uridylyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,28414
Polymers134,1653
Non-polymers1,11911
Water39622
1
A: Terminal uridylyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9794
Polymers44,7221
Non-polymers2583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Terminal uridylyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1375
Polymers44,7221
Non-polymers4154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Terminal uridylyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1685
Polymers44,7221
Non-polymers4464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-134 kcal/mol
Surface area47330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.232, 141.232, 174.475
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resseq 987:995 or resseq 997 or resseq...
21(chain C and (resseq 987:995 or resseq 997 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain B and (resseq 987:995 or resseq 997 or resseq...B0
211(chain C and (resseq 987:995 or resseq 997 or resseq...C0

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Components

#1: Protein Terminal uridylyltransferase 7 / TUT7 / TUTase 7 / Zinc finger CCHC domain-containing protein 6


Mass: 44721.812 Da / Num. of mol.: 3
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.74 Å3/Da / Density % sol: 67.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.8-1.0 M lithium sulfate, 0.075-0.2 M potassium iodide, 0.05-0.2 M trisodium citrate, pH 5-6
PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 59600 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 66.39 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Net I/σ(I): 32.8
Reflection shellResolution: 2.6→2.62 Å / Rmerge(I) obs: 0.597 / CC1/2: 0.828

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.614→61.155 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 28.52
RfactorNum. reflection% reflection
Rfree0.255 3006 5.05 %
Rwork0.2305 --
obs0.2317 59520 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 378.23 Å2 / Biso mean: 95.1683 Å2 / Biso min: 37.7 Å2
Refinement stepCycle: final / Resolution: 2.614→61.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8361 0 39 22 8422
Biso mean--103.65 59.89 -
Num. residues----1036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038588
X-RAY DIFFRACTIONf_angle_d0.60311610
X-RAY DIFFRACTIONf_chiral_restr0.0421286
X-RAY DIFFRACTIONf_plane_restr0.0041475
X-RAY DIFFRACTIONf_dihedral_angle_d12.6065155
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B3486X-RAY DIFFRACTION5.793TORSIONAL
12C3486X-RAY DIFFRACTION5.793TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6135-2.65640.33181380.30642649278799
2.6564-2.70220.28871330.293527022835100
2.7022-2.75130.3031460.28726452791100
2.7513-2.80420.31911440.280426992843100
2.8042-2.86150.31611400.28926802820100
2.8615-2.92370.29761400.314426982838100
2.9237-2.99170.38431380.305127082846100
2.9917-3.06650.31061490.304926772826100
3.0665-3.14940.36471280.284726782806100
3.1494-3.24210.28671680.277626592827100
3.2421-3.34670.28161470.265827032850100
3.3467-3.46630.27141420.258726672809100
3.4663-3.60510.25191500.253727062856100
3.6051-3.76920.25411490.237926792828100
3.7692-3.96780.23771390.210726952834100
3.9678-4.21640.22331410.202327032844100
4.2164-4.54180.22231490.189527002849100
4.5418-4.99870.22571390.183327112850100
4.9987-5.72160.22581320.206227072839100
5.7216-7.20680.24421460.240127132859100
7.2068-61.1720.24141480.203627352883100
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)
15.49980.71963.4730.57710.69885.57960.0213-0.80750.55830.0514-0.31210.1221-0.2539-0.79520.22580.54010.07030.05980.3261-0.04940.52771.3808-50.877619.3572
23.49590.83284.71765.84244.10238.0601-0.0867-0.5721.33750.3022-0.41240.1893-0.398-0.19140.53640.6228-0.0685-0.03770.487-0.00580.636920.4008-43.314726.8117
39.75424.022-2.56644.3815-2.19639.0203-0.1947-0.39190.0071-0.17430.1526-0.38670.55980.52170.0150.5429-0.0059-0.06140.5815-0.07730.458725.1805-52.62729.2298
45.59010.61230.38375.8290.92053.9516-0.12580.11.01390.0069-0.0535-0.4906-0.77060.46170.1980.4893-0.0561-0.07980.44060.0670.49846.8752-41.15846.9116
53.99781.82344.19522.33965.48727.52930.3060.622-0.1609-0.74550.1759-1.4785-0.46031.1636-0.40080.5454-0.07340.09490.92120.13720.836819.7176-46.46452.4253
67.41370.937-1.01825.82-1.6724.7320.28030.3273-1.1309-0.3902-0.2234-0.09430.53340.1098-0.07760.51060.0918-0.05790.4962-0.0240.4625-0.2525-63.31974.2895
73.1613-3.19251.23926.9196-1.47812.99630.3037-0.22790.1776-0.98220.08580.44220.2886-0.4256-0.40450.4156-0.02350.06790.71910.05340.5229-7.2086-54.06639.1599
82.5679-0.51360.93874.33-3.38447.46520.03990.02960.11980.0353-0.3619-0.1876-0.25420.63930.35010.6007-0.04330.00650.68870.00450.42828.0243-65.6253.394
93.41211.2105-0.13783.1869-1.1194.87270.1388-0.5150.48570.5636-0.04010.2594-0.8677-0.1566-0.1090.7310.09430.04650.5214-0.11460.5727-5.1685-42.063748.0151
102.7471.7085-0.43756.5076-0.264.58820.11120.19610.47140.3948-0.00761.0003-0.6178-0.9477-0.02650.47830.08920.01330.70590.07960.5563-21.149-68.504128.7629
118.6323-4.340.45673.3531-0.01560.62550.00660.31620.00160.05660.0036-0.1290.25410.0244-0.02510.57-0.0205-0.00580.54030.07120.338312.0613-77.294718.6101
125.5357-1.47161.50712.08962.19954.83140.1211-0.4643-0.39970.08220.3827-0.26111.1610.0585-0.49980.86390.068-0.05360.85440.07890.62620.1715-81.811829.2078
136.51160.82182.60258.16825.58297.456-0.0643-0.3948-0.15350.9379-0.11610.47840.55260.39960.26010.43050.02350.02290.50580.03970.356212.6438-76.970126.5127
143.6214-1.6675-2.61015.40041.50111.76190.022-0.14440.06410.35110.0599-0.04260.22290.0883-0.09460.4942-0.09810.03660.48860.05210.3247-9.2835-80.33724.8988
153.9751-5.4572-1.68997.33732.52753.42150.04320.3518-0.2598-0.5262-0.2109-0.00490.4182-0.65560.1660.5966-0.17540.0610.5442-0.02860.4172-10.3632-88.56828.5594
164.307-1.7926-3.00944.49430.64796.5375-0.19270.97690.1271-0.3324-0.08980.82630.481-1.39090.25420.4102-0.1158-0.02210.77530.03090.5693-23.3453-78.954421.6318
176.91982.0819-2.6822.16960.29048.2667-0.6891-0.32-0.76780.18270.11181.05743.0016-0.89650.75271.1308-0.13930.14730.6630.13110.7117-17.9139-95.917224.7384
184.6063-3.8525-3.17886.88647.32268.319-0.0303-0.4392-0.48410.6510.66680.62051.0501-0.8587-0.7380.8172-0.01010.15740.58410.2070.5312-7.851-94.347327.9895
196.5898-3.56416.94783.678-2.53667.35680.4968-0.9301-0.0028-0.3925-0.35680.05160.66610.085-0.14960.9157-0.13730.25210.75950.16210.5342-18.279-81.923439.8799
202.36542.0176-4.27165.88421.98654.00940.346-0.59160.48031.8005-0.3310.9984-0.9397-0.32710.09180.8061-0.02230.07310.7556-0.15760.6381-18.3537-68.21540.8709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 985 through 1035 )B985 - 1035
2X-RAY DIFFRACTION2chain 'B' and (resid 1036 through 1075 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 1076 through 1126 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 1127 through 1271 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 1272 through 1293 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1294 through 1342 )B0
7X-RAY DIFFRACTION7chain 'A' and (resid 986 through 1035 )A986 - 1035
8X-RAY DIFFRACTION8chain 'A' and (resid 1036 through 1124 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1125 through 1361 )A0
10X-RAY DIFFRACTION10chain 'C' and (resid 986 through 1015 )C986 - 1015
11X-RAY DIFFRACTION11chain 'C' and (resid 1016 through 1076 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 1077 through 1105 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 1106 through 1125 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 1126 through 1183 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 1184 through 1223 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 1224 through 1247 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 1248 through 1269 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 1270 through 1293 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 1294 through 1312 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 1313 through 1343 )C0

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