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- EMDB-17084: Structure of human terminal uridylyltransferase 7 (hTUT7/ZCCHC6) ... -

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Basic information

Entry
Database: EMDB / ID: EMD-17084
TitleStructure of human terminal uridylyltransferase 7 (hTUT7/ZCCHC6) bound with pre-let7g miRNA and UTPalphaS
Map dataHuman terminal uridylyltransferase 7 (TUT7, ZCCHC6) in complex with pre-let7g miRNA
Sample
  • Complex: human terminal urildylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA
    • Complex: Terminal uridylyltransferase 7
      • Protein or peptide: Terminal uridylyltransferase 7
    • Complex: RNA (25-MER)
      • RNA: RNA (25-MER)
  • Ligand: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate
KeywordsPolymerase / uridylation / RNA maturation and turnover control / RNA
Function / homology
Function and homology information


polyuridylation-dependent mRNA catabolic process / transposable element silencing by mRNA destabilization / RNA 3'-end processing / uridylyltransferase activity / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA metabolic process / Deadenylation of mRNA ...polyuridylation-dependent mRNA catabolic process / transposable element silencing by mRNA destabilization / RNA 3'-end processing / uridylyltransferase activity / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA metabolic process / Deadenylation of mRNA / pre-miRNA processing / oocyte maturation / miRNA binding / Zygotic genome activation (ZGA) / RNA binding / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger C2H2 type domain signature. / Nucleotidyltransferase superfamily ...Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger C2H2 type domain signature. / Nucleotidyltransferase superfamily / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Terminal uridylyltransferase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsYi G / Ye M / Gilbert RJ
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs.
Authors: Gangshun Yi / Mingda Ye / Loic Carrique / Afaf El-Sagheer / Tom Brown / Chris J Norbury / Peijun Zhang / Robert J C Gilbert /
Abstract: Tumor-suppressor let-7 pre-microRNAs (miRNAs) are regulated by terminal uridylyltransferases TUT7 and TUT4 that either promote let-7 maturation by adding a single uridine nucleotide to the pre-miRNA ...Tumor-suppressor let-7 pre-microRNAs (miRNAs) are regulated by terminal uridylyltransferases TUT7 and TUT4 that either promote let-7 maturation by adding a single uridine nucleotide to the pre-miRNA 3' end or mark them for degradation by the addition of multiple uridines. Oligo-uridylation is increased in cells by enhanced TUT7/4 expression and especially by the RNA-binding pluripotency factor LIN28A. Using cryogenic electron microscopy, we captured high-resolution structures of active forms of TUT7 alone, of TUT7 plus pre-miRNA and of both TUT7 and TUT4 bound with pre-miRNA and LIN28A. Our structures reveal that pre-miRNAs engage the enzymes in fundamentally different ways depending on the presence of LIN28A, which clamps them onto the TUTs to enable processive 3' oligo-uridylation. This study reveals the molecular basis for mono- versus oligo-uridylation by TUT7/4, as determined by the presence of LIN28A, and thus their mechanism of action in the regulation of cell fate and in cancer.
History
DepositionApr 7, 2023-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17084.png

Downloads & links

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Map

FileDownload / File: emd_17084.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman terminal uridylyltransferase 7 (TUT7, ZCCHC6) in complex with pre-let7g miRNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 280 pix.
= 260.96 Å		0.93 Å/pix.
x 280 pix.
= 260.96 Å		0.93 Å/pix.
x 280 pix.
= 260.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.234
Minimum - Maximum-0.0015942624 - 2.2518158
Average (Standard dev.)0.0014160931 (±0.027156932)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 260.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Human terminal uridylyltransferase 7 (TUT7, ZCCHC6) in complex...

Fileemd_17084_half_map_1.map
AnnotationHuman terminal uridylyltransferase 7 (TUT7, ZCCHC6) in complex with pre-let7g miRNA, half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human terminal uridylyltransferase 7 (TUT7, ZCCHC6) in complex...

Fileemd_17084_half_map_2.map
AnnotationHuman terminal uridylyltransferase 7 (TUT7, ZCCHC6) in complex with pre-let7g miRNA, half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human terminal urildylyltransferase 7 (TUT7/ZCCHC6) bound with pr...

EntireName: human terminal urildylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA
Components
  • Complex: human terminal urildylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA
    • Complex: Terminal uridylyltransferase 7
      • Protein or peptide: Terminal uridylyltransferase 7
    • Complex: RNA (25-MER)
      • RNA: RNA (25-MER)
  • Ligand: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate

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Supramolecule #1: human terminal urildylyltransferase 7 (TUT7/ZCCHC6) bound with pr...

SupramoleculeName: human terminal urildylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Terminal uridylyltransferase 7

SupramoleculeName: Terminal uridylyltransferase 7 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: RNA (25-MER)

SupramoleculeName: RNA (25-MER) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Terminal uridylyltransferase 7

MacromoleculeName: Terminal uridylyltransferase 7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA uridylyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 171.493766 KDa
Recombinant expressionOrganism: Escherichia coli KRX (bacteria)
SequenceString: MGDTAKPYFV KRTKDRGTMD DDDFRRGHPQ QDYLIIDDHA KGHGSKMEKG LQKKKITPGN YGNTPRKGPC AVSSNPYAFK NPIYSQPAW MNDSHKDQSK RWLSDEHTGN SDNWREFKPG PRIPVINRQR KDSFQENEDG YRWQDTRGCR TVRRLFHKDL T SLETTSEM ...String:
MGDTAKPYFV KRTKDRGTMD DDDFRRGHPQ QDYLIIDDHA KGHGSKMEKG LQKKKITPGN YGNTPRKGPC AVSSNPYAFK NPIYSQPAW MNDSHKDQSK RWLSDEHTGN SDNWREFKPG PRIPVINRQR KDSFQENEDG YRWQDTRGCR TVRRLFHKDL T SLETTSEM EAGSPENKKQ RSRPRKPRKT RNEENEQDGD LEGPVIDESV LSTKELLGLQ QAEERLKRDC IDRLKRRPRN YP TAKYTCR LCDVLIESIA FAHKHIKEKR HKKNIKEKQE EELLTTLPPP TPSQINAVGI AIDKVVQEFG LHNENLEQRL EIK RIMENV FQHKLPDCSL RLYGSSCSRL GFKNSDVNID IQFPAIMSQP DVLLLVQECL KNSDSFIDVD ADFHARVPVV VCRE KQSGL LCKVSAGNEN ACLTTKHLTA LGKLEPKLVP LVIAFRYWAK LCSIDRPEEG GLPPYVFALM AIFFLQQRKE PLLPV YLGS WIEGFSLSKL GNFNLQDIEK DVVIWEHTDS AAGDTGITKE EAPRETPIKR GQVSLILDVK HQPSVPVGQL WVELLR FYA LEFNLADLVI SIRVKELVSR ELKDWPKKRI AIEDPYSVKR NVARTLNSQP VFEYILHCLR TTYKYFALPH KITKSSL LK PLNAITCISE HSKEVINHHP DVQTKDDKLK NSVLAQGPGA TSSAANTCKV QPLTLKETAE SFGSPPKEEM GNEHISVH P ENSDCIQADV NSDDYKGDKV YHPETGRKNE KEKVGRKGKH LLTVDQKRGE HVVCGSTRNN ESESTLDLEG FQNPTAKEC EGLATLDNKA DLDGESTEGT EELEDSLNHF THSVQGQTSE MIPSDEEEED DEEEEEEEEP RLTINQREDE DGMANEDELD NTYTGSGDE DALSEEDDEL GEAAKYEDVK ECGKHVERAL LVELNKISLK EENVCEEKNS PVDQSDFFYE FSKLIFTKGK S PTVVCSLC KREGHLKKDC PEDFKRIQLE PLPPLTPKFL NILDQVCIQC YKDFSPTIIE DQAREHIRQN LESFIRQDFP GT KLSLFGS SKNGFGFKQS DLDVCMTING LETAEGLDCV RTIEELARVL RKHSGLRNIL PITTAKVPIV KFFHLRSGLE VDI SLYNTL ALHNTRLLSA YSAIDPRVKY LCYTMKVFTK MCDIGDASRG SLSSYAYTLM VLYFLQQRNP PVIPVLQEIY KGEK KPEIF VDGWNIYFFD QIDELPTYWS ECGKNTESVG QLWLGLLRFY TEEFDFKEHV ISIRRKSLLT TFKKQWTSKY IVIED PFDL NHNLGAGLSR KMTNFIMKAF INGRRVFGIP VKGFPKDYPS KMEYFFDPDV LTEGELAPND RCCRICGKIG HFMKDC PMR RKVRRRRDQE DALNQRYPEN KEKRSKEDKE IHNKYTEREV STKEDKPIQC TPQKAKPMRA AADLGREKIL RPPVEKW KR QDDKDLREKR CFICGREGHI KKECPQFKGS SGSLSSKYMT QGKASAKRTQ QES

UniProtKB: Terminal uridylyltransferase 7

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Macromolecule #2: RNA (25-MER)

MacromoleculeName: RNA (25-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.007763 KDa
SequenceString:
UGAGGUAGUA GUGCCACUGC CUUGC

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Macromolecule #3: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-...

MacromoleculeName: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate
type: ligand / ID: 3 / Number of copies: 1 / Formula: P5E
Molecular weightTheoretical: 500.207 Da
Chemical component information

ChemComp-P5E:
[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate

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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

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 256661
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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