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- PDB-9w4r: Cryo-EM structure of hTUT4_mini:hLin28A:pre-let-7g miRNA_UUU, con... -

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Basic information

Entry
Database: PDB / ID: 9w4r
TitleCryo-EM structure of hTUT4_mini:hLin28A:pre-let-7g miRNA_UUU, conformation 1
Components
  • Protein lin-28 homolog A
  • Terminal uridylyltransferase 4
  • pre-let-7g miRNA
KeywordsTRANSFERASE / Complex / TUTase
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 / miRNA catabolic process / protein-RNA adaptor activity / RNA uridylyltransferase / RNA 3'-end processing / pre-miRNA binding ...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 / miRNA catabolic process / protein-RNA adaptor activity / RNA uridylyltransferase / RNA 3'-end processing / 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 ribonucleoprotein granule / 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 / extracellular space / RNA binding / extracellular exosome / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
TUTase nucleotidyltransferase domain / : / : / Lin-28A-like, second zinc knuckle / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Cold-shock protein, DNA-binding ...TUTase nucleotidyltransferase domain / : / : / Lin-28A-like, second zinc knuckle / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleotidyltransferase superfamily / Zinc finger C2H2 type domain signature. / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / Terminal uridylyltransferase 4 / Protein lin-28 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsHan, X. / Yamashita, S. / Tomita, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Structural basis of Lin28-dependent pre-let-7 oligo-uridylylation by TUT4
Authors: Han, X. / Yamashita, S. / Tomita, K.
History
DepositionAug 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terminal uridylyltransferase 4
B: Protein lin-28 homolog A
C: pre-let-7g miRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,2187
Polymers177,9573
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Terminal uridylyltransferase 4 / TUTase 4 / Zinc finger CCHC domain-containing protein 11


Mass: 128071.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: human TUT4 (residues 202-1313) was cloned into pET29a vector with NdeI and XhoI sites. LEHHHHHH is the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: TUT4, KIAA0191, ZCCHC11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TAX3, RNA uridylyltransferase
#2: Protein Protein lin-28 homolog A / Lin-28A / Zinc finger CCHC domain-containing protein 1


Mass: 23850.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: human Lin28A(full-length, residues 1-209) was cloned into pET28b vector with NdeI and XhoI sites. LEHHHHHH is the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: LIN28A, CSDD1, LIN28, ZCCHC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H9Z2
#3: RNA chain pre-let-7g miRNA


Mass: 26035.369 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: human pre-let-7g miRNA containing additional 3'-UUU
Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of hTUT4: hLin28A: pre-let-7g / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solution
IDSpecimen-IDpH
117
227
Specimen
IDConc. (mg/ml)Experiment-IDEmbedding appliedShadowing appliedStaining appliedVitrification applied
10.71NONONOYES
20.71NONONOYES
Specimen support
IDSpecimen-IDGrid materialGrid mesh size (divisions/in.)Grid type
11COPPER300Quantifoil R1.2/1.3
22GOLD300UltrAuFoil R1.2/1.3
Vitrification
IDCryogen nameHumidity (%)Specimen-IDEntry-ID
1ETHANE10019W4R
2ETHANE10029W4R

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Accelerating voltage: 300 kV / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Model: TFS KRIOS / Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm

IDSpecimen-ID
11
22
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector modelNum. of grids imagedNum. of real imagesDetails
1150GATAN K3 BIOQUANTUM (6k x 4k)324091Three datasets with Quantifoil Cu grids.
2250GATAN K3 BIOQUANTUM (6k x 4k)213672Two datasets with UltrAufoil grids.

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192885 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 265.73 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00388607
ELECTRON MICROSCOPYf_angle_d0.761811879
ELECTRON MICROSCOPYf_chiral_restr0.04691354
ELECTRON MICROSCOPYf_plane_restr0.00641302
ELECTRON MICROSCOPYf_dihedral_angle_d26.23813450

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