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- PDB-6iw6: Crystal structure of the Lin28-interacting module of human TUT4 -

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Basic information

Entry
Database: PDB / ID: 6iw6
TitleCrystal structure of the Lin28-interacting module of human TUT4
ComponentsTerminal uridylyltransferase 4,Terminal uridylyltransferase 4
KeywordsTRANSFERASE / TUT4
Function / homology
Function and homology information


polyuridylation-dependent mRNA catabolic process / retrotransposon silencing by mRNA destabilization / RNA 3'-end processing / RNA 3' uridylation / RNA uridylyltransferase / miRNA catabolic process / RNA uridylyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA metabolic process / Deadenylation of mRNA ...polyuridylation-dependent mRNA catabolic process / retrotransposon silencing by mRNA destabilization / RNA 3'-end processing / RNA 3' uridylation / RNA uridylyltransferase / miRNA catabolic process / 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 / stem cell population maintenance / Zygotic genome activation (ZGA) / cytoplasmic ribonucleoprotein granule / nucleolus / RNA binding / extracellular space / zinc ion binding / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Zinc finger C2H2 type domain signature. / Nucleotidyltransferase superfamily / zinc finger / Zinc knuckle ...TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / 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
CITRATE ANION / Terminal uridylyltransferase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsYamashita, S. / Tomita, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceLS135 Japan
Japan Society for the Promotion of Science18H03980 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)26113002 Japan
CitationJournal: Nat Commun / Year: 2019
Title: Crystal structure of the Lin28-interacting module of human terminal uridylyltransferase that regulates let-7 expression.
Authors: Yamashita, S. / Nagaike, T. / Tomita, K.
History
DepositionDec 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2May 15, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 22, 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 4,Terminal uridylyltransferase 4
B: Terminal uridylyltransferase 4,Terminal uridylyltransferase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,65816
Polymers103,5222
Non-polymers1,13614
Water1,60389
1
A: Terminal uridylyltransferase 4,Terminal uridylyltransferase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2677
Polymers51,7611
Non-polymers5066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint1 kcal/mol
Surface area23140 Å2
MethodPISA
2
B: Terminal uridylyltransferase 4,Terminal uridylyltransferase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3919
Polymers51,7611
Non-polymers6308
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint0 kcal/mol
Surface area23180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.270, 127.830, 168.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Terminal uridylyltransferase 4,Terminal uridylyltransferase 4 / TUTase 4 / Zinc finger CCHC domain-containing protein 11


Mass: 51760.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUT4, KIAA0191, ZCCHC11 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TAX3, RNA uridylyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM Hepes-NaOH, pH 7.0, 20% (w/v) PEG 3350, 3% MPD, 200 mM Ammonium Citrate and 3% (w/v) 1,5-Diaminopentane dihydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→19.963 Å / Num. obs: 48018 / % possible obs: 99.9 % / Redundancy: 26.831 % / Biso Wilson estimate: 49.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.19 / Rrim(I) all: 0.194 / Χ2: 0.988 / Net I/σ(I): 18.11 / Num. measured all: 1288392 / Scaling rejects: 40
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.4626.1442.3721.6991032350534820.7622.41999.3
2.46-2.5327.1761.9972.1192753341334130.8592.035100
2.53-2.6127.1861.6042.6590802334033400.8811.635100
2.61-2.6927.2251.2583.4688236324132410.9531.282100
2.69-2.7726.9771.0694.1385004315131510.9551.089100
2.77-2.8727.150.8675.1682400303530350.9720.883100
2.87-2.9827.0770.7046.3879770294629460.980.717100
2.98-3.126.8180.5568.0275493281528150.9870.567100
3.1-3.2426.8450.43610.2373287273127300.9920.444100
3.24-3.426.9680.31913.6669983259525950.9960.325100
3.4-3.5827.30.19620.6767595247624760.9980.2100
3.58-3.827.5290.14726.1465105236523650.9990.15100
3.8-4.0626.7450.11131.7558999220622060.9990.113100
4.06-4.3926.5530.0841.01549382069206910.082100
4.39-4.827.3420.06649523331914191410.067100
4.8-5.3727.2840.06748.51473371735173510.068100
5.37-6.225.6070.07543.38394601541154110.076100
6.2-7.626.1270.0652.24345921324132410.061100
7.6-10.7425.4380.03772.73264551040104010.038100
10.74-19.96321.3630.03375.891281861160010.03498.2

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Processing

Software
NameVersionClassification
PHENIX1.12-2829_1309refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W0N

5w0n


Resolution: 2.402→19.963 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2371 2392 5 %
Rwork0.21 45471 -
obs0.2113 47863 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 252.82 Å2 / Biso mean: 69.8829 Å2 / Biso min: 25.87 Å2
Refinement stepCycle: final / Resolution: 2.402→19.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7134 0 62 89 7285
Biso mean--76.25 50.51 -
Num. residues----876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017342
X-RAY DIFFRACTIONf_angle_d0.9989908
X-RAY DIFFRACTIONf_chiral_restr0.1651098
X-RAY DIFFRACTIONf_plane_restr0.0071264
X-RAY DIFFRACTIONf_dihedral_angle_d17.6482808
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4022-2.45110.351370.36992630276799
2.4511-2.50430.33351400.318226432783100
2.5043-2.56250.36741380.298926412779100
2.5625-2.62640.30991380.282726332771100
2.6264-2.69730.30921400.260326602800100
2.6973-2.77640.29281400.261526562796100
2.7764-2.86580.30641400.26726542794100
2.8658-2.96790.26151400.249126502790100
2.9679-3.08630.31741400.245426622802100
3.0863-3.22620.3091410.251426752816100
3.2262-3.39560.2891400.242926612801100
3.3956-3.60710.22351400.208926682808100
3.6071-3.88380.22861420.200827052847100
3.8838-4.27110.19881420.178826912833100
4.2711-4.88130.18021420.165326912833100
4.8813-6.12030.22361440.181327312875100
6.1203-19.9640.16711480.162820296899
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)
12.207-1.74643.26224.0719-3.76682.4981-0.10770.07150.3283-0.44680.00230.27830.10490.10980.10170.45360.02240.06570.45570.06150.5572-25.260345.8129-9.5841
20.9345-0.030.07182.4134-0.26361.683-0.0089-0.1745-0.09290.2134-0.00860.561-0.0232-0.18260.04670.30020.04640.08220.3849-0.02770.5127-14.833517.808718.14
33.96450.79090.7613.2226-0.24132.66860.127-0.6817-0.05980.9602-0.2308-0.38570.04530.28390.1010.62320.0422-0.02960.43360.02970.4144.234815.641830.5551
41.92184.1096-2.4087.3457-3.59910.8712-0.48720.4948-0.49110.07950.5136-1.2177-0.2241-0.1327-0.02320.6778-0.0895-0.05920.5776-0.16160.7154-21.1602-45.910510.7417
50.9538-0.2015-0.0022.40360.27572.4886-0.06950.08070.117-0.0683-0.00240.5737-0.0355-0.20130.07440.2456-0.0325-0.03180.33770.00210.4459-14.8118-17.8075-14.0438
63.8249-0.5455-1.14882.18820.64182.15230.02440.74730.123-0.6966-0.024-0.0785-0.0385-0.0066-0.0030.515-0.048-0.02310.46430.01490.36164.1449-15.7304-26.5267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 255 through 348 )A255 - 348
2X-RAY DIFFRACTION2(chain 'A' and (resid 349 through 369 )) or (chain 'A' and (resid 517 through 731 ))A0
3X-RAY DIFFRACTION3chain 'A' and (resid 370 through 516 )A370 - 516
4X-RAY DIFFRACTION4chain 'B' and (resid 255 through 348 )B255 - 348
5X-RAY DIFFRACTION5(chain 'B' and (resid 349 through 369 )) or (chain 'B' and (resid 517 through 731 ))B0
6X-RAY DIFFRACTION6chain 'B' and (resid 370 through 516 )B370 - 516

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