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- EMDB-65643: Cryo-EM structure of hTUT4_mini:hLin28A:pre-let-7g miRNA_UUU, con... -

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Basic information

Entry
Database: EMDB / ID: EMD-65643
TitleCryo-EM structure of hTUT4_mini:hLin28A:pre-let-7g miRNA_UUU, conformation 2
Map dataprimary map (postprocessed with EMReady)
Sample
  • Complex: Complex of hTUT4:hLin28A:pre-let-7g
    • Protein or peptide: Terminal uridylyltransferase 4
    • Protein or peptide: Protein lin-28 homolog A
    • RNA: pre-let-7g miRNA
  • Ligand: ZINC ION
KeywordsComplex / TUTase / TRANSFERASE
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
Terminal uridylyltransferase 4 / Protein lin-28 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsHan X / Yamashita S / Tomita K
Funding support Japan, 1 items
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, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65643.png

Downloads & links

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Map

FileDownload / File: emd_65643.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map (postprocessed with EMReady)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 128 pix.
= 159.36 Å		1.25 Å/pix.
x 128 pix.
= 159.36 Å		1.25 Å/pix.
x 128 pix.
= 159.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-0.08587314 - 10.880281
Average (Standard dev.)0.016279284 (±0.47703862)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 159.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65643_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_65643_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_65643_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of hTUT4:hLin28A:pre-let-7g

EntireName: Complex of hTUT4:hLin28A:pre-let-7g
Components
  • Complex: Complex of hTUT4:hLin28A:pre-let-7g
    • Protein or peptide: Terminal uridylyltransferase 4
    • Protein or peptide: Protein lin-28 homolog A
    • RNA: pre-let-7g miRNA
  • Ligand: ZINC ION

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Supramolecule #1: Complex of hTUT4:hLin28A:pre-let-7g

SupramoleculeName: Complex of hTUT4:hLin28A:pre-let-7g / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Terminal uridylyltransferase 4

MacromoleculeName: Terminal uridylyltransferase 4 / type: protein_or_peptide / ID: 1
Details: human TUT4(residues 202-1313) was cloned into pET29a with NdeI and XhoI site. LEHHHHHH is the expression tag. The C-terminal half was not modeled due to the insufficient potential map.
Number of copies: 1 / Enantiomer: LEVO / EC number: RNA uridylyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 128.071117 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEKCALQNSP RSQKQQTCTD NTGDSDDSAS GIEDVSDDLS KMKNDESNKE NSSEMDYLEN ATVIDESALT PEQRLGLKQA EERLERDHI FRLEKRSPEY TNCRYLCKLC LIHIENIQGA HKHIKEKRHK KNILEKQEES ELRSLPPPSP AHLAALSVAV I ELAKEHGI ...String:
MEKCALQNSP RSQKQQTCTD NTGDSDDSAS GIEDVSDDLS KMKNDESNKE NSSEMDYLEN ATVIDESALT PEQRLGLKQA EERLERDHI FRLEKRSPEY TNCRYLCKLC LIHIENIQGA HKHIKEKRHK KNILEKQEES ELRSLPPPSP AHLAALSVAV I ELAKEHGI TDDDLRVRQE IVEEMSKVIT TFLPECSLRL YGSSLTRFAL KSSDVNIDIK FPPKMNHPDL LIKVLGILKK NV LYVDVES DFHAKVPVVV CRDRKSGLLC RVSAGNDMAC LTTDLLTALG KIEPVFIPLV LAFRYWAKLC YIDSQTDGGI PSY CFALMV MFFLQQRKPP LLPCLLGSWI EGFDPKRMDD FQLKGIVEEK FVKWECNSSS ATEKNSIAEE NKAKADQPKD DTKK TETDN QSNAMKEKHG KSPLALETPN RVSLGQLWLE LLKFYTLDFA LEEYVICVRI QDILTRENKN WPKRRIAIED PFSVK RNVA RSLNSQLVYE YVVERFRAAY RYFACPQTKG GNKSTVDFKK REKGKISNKK PVKSNNMATN GCILLGETTE KINAER EQP VQCDEMDCTS QRCIIDNNNL LVNELDFADH GQDSSSLSTS KSSEIEPKLD KKQDDLAPSE TCLKKELSQC NCIDLSK SP DPDKSTGTDC RSNLETESSH QSVCTDTSAT SCNCKATEDA SDLNDDDNLP TQELYYVFDK FILTSGKPPT IVCSICKK D GHSKNDCPED FRKIDLKPLP PMTNRFREIL DLVCKRCFDE LSPPCSEQHN REQILIGLEK FIQKEYDEKA RLCLFGSSK NGFGFRDSDL DICMTLEGHE NAEKLNCKEI IENLAKILKR HPGLRNILPI TTAKVPIVKF EHRRSGLEGD ISLYNTLAQH NTRMLATYA AIDPRVQYLG YTMKVFAKRC DIGDASRGSL SSYAYILMVL YFLQQRKPPV IPVLQEIFDG KQIPQRMVDG W NAFFFDKT EELKKRLPSL GKNTESLGEL WLGLLRFYTE EFDFKEYVIS IRQKKLLTTF EKQWTSKCIA IEDPFDLNHN LG AGVSRKM TNFIMKAFIN GRKLFGTPFY PLIGREAEYF FDSRVLTDGE LAPNDRCCRV CGKIGHYMKD CPKRKSLEHH HHH H

UniProtKB: Terminal uridylyltransferase 4

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Macromolecule #2: Protein lin-28 homolog A

MacromoleculeName: Protein lin-28 homolog A / type: protein_or_peptide / ID: 2
Details: human Lin28A (full-length, residues 1-209) was cloned into pET28b with NdeI and XhoI site. LEHHHHHH is the expression tag.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.850129 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSVSNQQFA GGCAKAAEEA PEEAPEDAAR AADEPQLLHG AGICKWFNVR MGFGFLSMTA RAGVALDPPV DVFVHQSKLH MEGFRSLKE GEAVEFTFKK SAKGLESIRV TGPGGVFCIG SERRPKGKSM QKRRSKGDRC YNCGGLDHHA KECKLPPQPK K CHFCQSIS ...String:
MGSVSNQQFA GGCAKAAEEA PEEAPEDAAR AADEPQLLHG AGICKWFNVR MGFGFLSMTA RAGVALDPPV DVFVHQSKLH MEGFRSLKE GEAVEFTFKK SAKGLESIRV TGPGGVFCIG SERRPKGKSM QKRRSKGDRC YNCGGLDHHA KECKLPPQPK K CHFCQSIS HMVASCPLKA QQGPSAQGKP TYFREEEEEI HSPTLLPEAQ NLEHHHHHH

UniProtKB: Protein lin-28 homolog A

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Macromolecule #3: pre-let-7g miRNA

MacromoleculeName: pre-let-7g miRNA / type: rna / ID: 3
Details: human pre-let-7g miRNA containing additional 3'-UUU.
Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.035369 KDa
SequenceString:
UGAGGUAGUA GUUUGUACAG UUUGAGGGUC UAUGAUACCA CCCGGUACAG GAGAUAACUG UACAGGCCAC UGCCUUGCUU U

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation #1

Preparation ID1
Concentration0.7 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Sample preparation #2

Preparation ID2
Concentration0.7 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy #1

Microscopy ID1
MicroscopeTFS KRIOS
Image recordingImage recording ID: 1 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 3 / Number real images: 24091 / Average electron dose: 50.0 e/Å2 / Details: Three datasets with Quantifoil Cu grids.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeTFS KRIOS
Image recordingImage recording ID: 2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 13672 / Average electron dose: 50.0 e/Å2 / Details: Two datasets with UltrAufoil grids.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 274962
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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