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Yorodumi- PDB-8ost: Structure of human terminal uridylyltransferase 4 (TUT4, ZCCHC11)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ost | ||||||
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Title | Structure of human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex with pre-let7g miRNA and Lin28A | ||||||
Components |
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Keywords | CELL CYCLE / Polymerase / uridylation / RNA maturation and turnover control / RNA | ||||||
Function / homology | Function and homology information negative regulation of glial cell differentiation / positive regulation of cell proliferation involved in kidney development / negative regulation of pre-miRNA processing / polyuridylation-dependent mRNA catabolic process / transposable element silencing by mRNA destabilization / RNA 3'-end processing / miRNA catabolic process / protein-RNA adaptor activity / RNA 3' uridylation / RNA uridylyltransferase ...negative regulation of glial cell differentiation / positive regulation of cell proliferation involved in kidney development / negative regulation of pre-miRNA processing / polyuridylation-dependent mRNA catabolic process / transposable element silencing by mRNA destabilization / RNA 3'-end processing / miRNA catabolic process / protein-RNA adaptor activity / RNA 3' uridylation / RNA uridylyltransferase / pre-miRNA binding / RNA uridylyltransferase activity / Transcriptional regulation of pluripotent stem cells / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA metabolic process / Deadenylation of mRNA / pre-miRNA processing / positive regulation of cytoplasmic translation / sequence-specific mRNA binding / oocyte maturation / miRNA binding / stem cell population maintenance / Zygotic genome activation (ZGA) / germ cell development / positive regulation of TOR signaling / rough endoplasmic reticulum / translation initiation factor binding / positive regulation of neuron differentiation / stem cell differentiation / cellular response to glucose stimulus / P-body / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / G-quadruplex RNA binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of translation / mRNA binding / nucleolus / RNA binding / extracellular space / extracellular exosome / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.69 Å | ||||||
Authors | Gilbert, R.J. / Yi, G. / Ye, M. | ||||||
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 | 8ost.cif.gz | 230 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ost.ent.gz | 163.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ost.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ost_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8ost_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8ost_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 8ost_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/8ost ftp://data.pdbj.org/pub/pdb/validation_reports/os/8ost | HTTPS FTP |
-Related structure data
Related structure data | 17164MC 8oefC 8oppC 8opsC 8optC 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: 185433.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TUT4, KIAA0191, ZCCHC11 / Production host: Escherichia coli KRX (bacteria) / References: UniProt: Q5TAX3, RNA uridylyltransferase | ||
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#2: Protein | Mass: 22778.975 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LIN28A, CSDD1, LIN28, ZCCHC1 / Production host: Escherichia coli KRX (bacteria) / References: UniProt: Q9H9Z2 | ||
#3: RNA chain | Mass: 22287.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 15281257 | ||
#4: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
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Source (recombinant) |
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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 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 186227 / Symmetry type: POINT | ||||||||||||||||||||||||
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