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- PDB-8opp: Structure of human terminal uridylyltransferase 7 (hTUT7/ZCCHC6) ... -

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Basic information

Entry
Database: PDB / ID: 8opp
TitleStructure of human terminal uridylyltransferase 7 (hTUT7/ZCCHC6) bound with pre-let7g miRNA and UTPalphaS
Components
  • RNA (25-MER)
  • Terminal uridylyltransferase 7
KeywordsRNA / Polymerase / uridylation / RNA maturation and turnover control
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
Chem-P5E / RNA / RNA (> 10) / Terminal uridylyltransferase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsYi, G. / Ye, M. / Gilbert, R.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs.
Authors: Gangshun Yi / Mingda Ye / Loic Carrique / Afaf El-Sagheer / Tom Brown / Chris J Norbury / Peijun Zhang / Robert J C Gilbert /
Abstract: Tumor-suppressor let-7 pre-microRNAs (miRNAs) are regulated by terminal uridylyltransferases TUT7 and TUT4 that either promote let-7 maturation by adding a single uridine nucleotide to the pre-miRNA ...Tumor-suppressor let-7 pre-microRNAs (miRNAs) are regulated by terminal uridylyltransferases TUT7 and TUT4 that either promote let-7 maturation by adding a single uridine nucleotide to the pre-miRNA 3' end or mark them for degradation by the addition of multiple uridines. Oligo-uridylation is increased in cells by enhanced TUT7/4 expression and especially by the RNA-binding pluripotency factor LIN28A. Using cryogenic electron microscopy, we captured high-resolution structures of active forms of TUT7 alone, of TUT7 plus pre-miRNA and of both TUT7 and TUT4 bound with pre-miRNA and LIN28A. Our structures reveal that pre-miRNAs engage the enzymes in fundamentally different ways depending on the presence of LIN28A, which clamps them onto the TUTs to enable processive 3' oligo-uridylation. This study reveals the molecular basis for mono- versus oligo-uridylation by TUT7/4, as determined by the presence of LIN28A, and thus their mechanism of action in the regulation of cell fate and in cancer.
History
DepositionApr 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
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Revision 1.1Aug 7, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Terminal uridylyltransferase 7
D: RNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,0023
Polymers179,5022
Non-polymers5001
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 171493.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUT7, HS2, KIAA1711, ZCCHC6 / Production host: Escherichia coli KRX (bacteria) / References: UniProt: Q5VYS8, RNA uridylyltransferase
#2: RNA chain RNA (25-MER)


Mass: 8007.763 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-P5E / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 500.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O14P3S
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1human terminal urildylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNACOMPLEX#1-#20MULTIPLE SOURCES
2Terminal uridylyltransferase 7COMPLEX#11RECOMBINANT
3RNA (25-MER)COMPLEX#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
22Escherichia coli KRX (bacteria)1452720KRX
33Synthetic construct (others)32630
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 256661 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026125
ELECTRON MICROSCOPYf_angle_d0.4678410
ELECTRON MICROSCOPYf_dihedral_angle_d9.831014
ELECTRON MICROSCOPYf_chiral_restr0.038974
ELECTRON MICROSCOPYf_plane_restr0.004963

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