+Open data
-Basic information
Entry | Database: PDB / ID: 8oef | ||||||
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Title | Structure of human terminal uridylyltransferase 7 (hTUT7/ZCCHC6) | ||||||
Components | Terminal uridylyltransferase 7 | ||||||
Keywords | RNA / Polymerase / uridylation / RNA maturation and turnover control | ||||||
Function / homology | Function and homology information polyuridylation-dependent mRNA catabolic process / retrotransposon silencing by mRNA destabilization / uridylyltransferase activity / RNA 3'-end processing / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / miRNA metabolic process / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA ...polyuridylation-dependent mRNA catabolic process / retrotransposon silencing by mRNA destabilization / uridylyltransferase activity / RNA 3'-end processing / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / miRNA metabolic process / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / pre-miRNA processing / miRNA binding / oocyte maturation / Zygotic genome activation (ZGA) / RNA binding / zinc ion binding / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Yi, G. / Ye, M. / Gilbert, R.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oef.cif.gz | 250.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oef.ent.gz | 188.3 KB | Display | PDB format |
PDBx/mmJSON format | 8oef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/8oef ftp://data.pdbj.org/pub/pdb/validation_reports/oe/8oef | HTTPS FTP |
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-Related structure data
Related structure data | 16825MC 8oppC 8opsC 8optC 8ostC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: human terminal urildylyltransferase 7 (TUT7/ZCCHC6) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: KRX |
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 273443 / Symmetry type: POINT | ||||||||||||||||||||||||
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