9W4R | pdb_00009w4r

Cryo-EM structure of hTUT4_mini:hLin28A:pre-let-7g miRNA_UUU, conformation 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanistic insights into Lin28-dependent oligo-uridylylation of pre-let-7 by TUT4.

Han, X.Yamashita, S.Tomita, K.

(2026) Nucleic Acids Res 54

  • DOI: https://doi.org/10.1093/nar/gkaf1421
  • Primary Citation of Related Structures:  
    9W4R, 9W4S

  • PubMed Abstract: 

    Lin28-dependent oligo-uridylylation of precursor let-7 (pre-let-7) by terminal uridylyltransferases 4 and 7 (TUT4/7) represses let-7 expression by blocking Dicer processing, thereby regulating cell differentiation and proliferation. The interaction between the Lin28:pre-let-7 complex and the N-terminal Lin28-interacting module (LIM) of TUT4/7 is required for pre-let-7 oligo-uridylylation by the C-terminal catalytic module (CM). Here, we report the cryogenic electron microscopy structure of human TUT4 complexed with Lin28A and oligo-uridylated pre-let-7, representing the elongation stage of oligo-uridylylation. Structural and biochemical analyses suggest that, after recruitment of pre-let-7 to the LIM through interactions between its terminal stem-loop and Lin28A, the CM associates with the LIM through protein-protein interactions. The double-stranded stem region of pre-let-7 is surrounded by the CM and LIM, the upper portion of the duplex unwinds, and the 3' end of pre-let-7 is positioned in the CM catalytic site for the initiation of oligo-uridylylation. At the oligo-uridylylation stage, the CM finger domain clamps the double-stranded region of pre-let-7, thereby further stabilizing the pre-let-7:TUT4 complex, enabling processive elongation of the uridine tail by the CM. Thus, the LIM functions as a stable anchor, working together with Lin28A to ensure efficient and processive oligo-uridylylation of pre-let-7.


  • Organizational Affiliation
    • Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Terminal uridylyltransferase 41,121Homo sapiensMutation(s): 0 
Gene Names: TUT4KIAA0191ZCCHC11
EC: 2.7.7.52
UniProt & NIH Common Fund Data Resources
Find proteins for Q5TAX3 (Homo sapiens)
Explore Q5TAX3 
Go to UniProtKB:  Q5TAX3
PHAROS:  Q5TAX3
GTEx:  ENSG00000134744 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5TAX3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein lin-28 homolog A217Homo sapiensMutation(s): 0 
Gene Names: LIN28ACSDD1LIN28ZCCHC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9Z2 (Homo sapiens)
Explore Q9H9Z2 
Go to UniProtKB:  Q9H9Z2
PHAROS:  Q9H9Z2
GTEx:  ENSG00000131914 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H9Z2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
pre-let-7g miRNA81Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Data collection, Database references
  • Version 1.2: 2026-01-28
    Changes: Data collection, Database references