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- EMDB-17087: Human terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre... -

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Basic information

Entry
Database: EMDB / ID: EMD-17087
TitleHuman terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 2
Map dataHuman terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 2
Sample
  • Complex: Human terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 2
    • Complex: Terminal uridylyltransferase 7 and Protein lin-28 homolog A
      • Protein or peptide: Terminal uridylyltransferase 7
      • Protein or peptide: Protein lin-28 homolog A
    • Complex: RNA (53-MER)
      • RNA: RNA (53-MER)
  • Ligand: ZINC ION
KeywordsPolymerase / uridylation / RNA maturation and turnover control / RNA BINDING PROTEIN
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 / RNA 3'-end processing / uridylyltransferase activity / miRNA catabolic process / protein-RNA adaptor activity / RNA 3' uridylation ...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 / RNA 3'-end processing / uridylyltransferase activity / miRNA catabolic process / protein-RNA adaptor activity / RNA 3' uridylation / RNA uridylyltransferase / 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 stress granule / G-quadruplex RNA binding / negative regulation of translation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Unstructured region 4 on terminal uridylyltransferase 7 / 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 ...Unstructured region 4 on terminal uridylyltransferase 7 / 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 / 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. / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Terminal uridylyltransferase 7 / Protein lin-28 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 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 8, 2023-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17087.png

Downloads & links

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Map

FileDownload / File: emd_17087.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 350 pix.
= 326.2 Å		0.93 Å/pix.
x 350 pix.
= 326.2 Å		0.93 Å/pix.
x 350 pix.
= 326.2 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: 0.0754
Minimum - Maximum-0.0042668222 - 2.171946
Average (Standard dev.)0.00082762074 (±0.020307876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 326.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Human terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g...

Fileemd_17087_half_map_1.map
AnnotationHuman terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 2 - half map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Human terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g...

Fileemd_17087_half_map_2.map
AnnotationHuman terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 2 - 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 uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre...

EntireName: Human terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 2
Components
  • Complex: Human terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 2
    • Complex: Terminal uridylyltransferase 7 and Protein lin-28 homolog A
      • Protein or peptide: Terminal uridylyltransferase 7
      • Protein or peptide: Protein lin-28 homolog A
    • Complex: RNA (53-MER)
      • RNA: RNA (53-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Human terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre...

SupramoleculeName: Human terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Terminal uridylyltransferase 7 and Protein lin-28 homolog A

SupramoleculeName: Terminal uridylyltransferase 7 and Protein lin-28 homolog A
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: RNA (53-MER)

SupramoleculeName: RNA (53-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 #3: Protein lin-28 homolog A

MacromoleculeName: Protein lin-28 homolog A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.778975 KDa
Recombinant expressionOrganism: Escherichia coli KRX (bacteria)
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 N

UniProtKB: Protein lin-28 homolog A

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Macromolecule #2: RNA (53-MER)

MacromoleculeName: RNA (53-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.457402 KDa
SequenceString:
UUGUACAGUU UGAGGGUAUA UGAUACAACC CGGUACAGGA GAUAACUGUA CAGG

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / 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

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: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 226379
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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