9W4R | pdb_00009w4r

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

• PDB DOI: https://doi.org/10.2210/pdb9W4R/pdb
• NAKB: 9W4R
• EM Map EMD-65642: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-08-01 Released: 2025-12-03 
• Deposition Author(s): Han, X., Yamashita, S., Tomita, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

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

Literature

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

Han, X., Yamashita, S., Tomita, K.

(2025) Nucleic Acids Res 

• DOI: https://doi.org/10.1093/nar/gkaf1421

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 178.22 kDa 
• Atom Count: 8,309 
• Modeled Residue Count: 936 
• Deposited Residue Count: 1,419 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terminal uridylyltransferase 4	A	1,121	Homo sapiens	Mutation(s): 0  Gene Names: TUT4, KIAA0191, ZCCHC11 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein lin-28 homolog A	B	217	Homo sapiens	Mutation(s): 0  Gene Names: LIN28A, CSDD1, LIN28, ZCCHC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9Z2 (Homo sapiens) Explore Q9H9Z2  Go to UniProtKB:  Q9H9Z2
PHAROS:  Q9H9Z2 GTEx:  ENSG00000131914

Entity ID: 3
Molecule	Chains	Length	Organism	Image
pre-let-7g miRNA	C	81	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Han, X., Yamashita, S., Tomita, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

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