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Yorodumi- PDB-8opt: Human terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8opt | ||||||
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Title | Human terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 2 | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / Polymerase / uridylation / RNA maturation and turnover control | ||||||
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 / retrotransposon silencing by mRNA destabilization / uridylyltransferase activity / protein-RNA adaptor activity / RNA 3'-end processing / miRNA catabolic process / RNA 3' uridylation ...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 / retrotransposon silencing by mRNA destabilization / uridylyltransferase activity / protein-RNA adaptor activity / RNA 3'-end processing / miRNA catabolic process / 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 / positive regulation of cytoplasmic translation / pre-miRNA processing / sequence-specific mRNA binding / oocyte maturation / miRNA binding / stem cell population maintenance / germ cell development / Zygotic genome activation (ZGA) / 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 / G-quadruplex RNA binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of translation / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å | ||||||
Authors | Yi, G. / Ye, M. / Gilbert, R.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat.Struct.Biol. / Year: 2024 Title: Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs Authors: Yi, G. / Ye, M. / Carrique, L. / El-Sagheer, A. / Brown, T. / Norbury, C.J. / Zhang, P. / Gilbert, R.J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8opt.cif.gz | 340.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8opt.ent.gz | 264.3 KB | Display | PDB format |
PDBx/mmJSON format | 8opt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8opt_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8opt_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8opt_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 8opt_validation.cif.gz | 62.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/8opt ftp://data.pdbj.org/pub/pdb/validation_reports/op/8opt | HTTPS FTP |
-Related structure data
Related structure data | 17087MC 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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#2: RNA chain | Mass: 17457.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||
#3: 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 | ||
#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
Component |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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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: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 226379 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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