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- EMDB-17164: Structure of human terminal uridylyltransferase 4 (TUT4, ZCCHC11)... -

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Basic information

Entry
Database: EMDB / ID: EMD-17164
TitleStructure of human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex with pre-let7g miRNA and Lin28A
Map dataHuman terminal uridylyltransferase 4 (TUT4; ZCCHC11) bound with pre-let7-g miRNA and Lin28A (equivalent to TUT7 complex 1)
Sample
  • Complex: Human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex with pre-let7g miRNA and Lin28A
    • Complex: Terminal uridylyltransferase 4 and Protein lin-28 homolog A
      • Protein or peptide: Terminal uridylyltransferase 4
      • Protein or peptide: Protein lin-28 homolog A
    • Complex: pre-let7-g
      • RNA: pre-let7-g
  • Ligand: ZINC ION
KeywordsPolymerase / uridylation / RNA maturation and turnover control / RNA / CELL CYCLE
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 / RNA 3'-end processing / transposable element silencing by mRNA destabilization / miRNA catabolic process / protein-RNA adaptor activity / RNA 3' uridylation / RNA uridylyltransferase ...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 / RNA 3'-end processing / transposable element silencing by mRNA destabilization / 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 ribonucleoprotein granule / 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 / extracellular space / 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 / 'Cold-shock' DNA-binding domain ...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 / 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 4 / Protein lin-28 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsGilbert RJ / Yi G / Ye M
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 20, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17164.png

Downloads & links

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Map

FileDownload / File: emd_17164.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman terminal uridylyltransferase 4 (TUT4; ZCCHC11) bound with pre-let7-g miRNA and Lin28A (equivalent to TUT7 complex 1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.111
Minimum - Maximum-1.138337 - 1.4244231
Average (Standard dev.)-0.00032405555 (±0.013177388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Human terminal uridylyltransferase 4 (TUT4; ZCCHC11) bound with...

Fileemd_17164_half_map_1.map
AnnotationHuman terminal uridylyltransferase 4 (TUT4; ZCCHC11) bound with pre-let7-g miRNA and Lin28A (equivalent to TUT7 complex 1) - 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 4 (TUT4; ZCCHC11) bound with...

Fileemd_17164_half_map_2.map
AnnotationHuman terminal uridylyltransferase 4 (TUT4; ZCCHC11) bound with pre-let7-g miRNA and Lin28A (equivalent to TUT7 complex 1) - 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 4 (TUT4, ZCCHC11) in complex w...

EntireName: Human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex with pre-let7g miRNA and Lin28A
Components
  • Complex: Human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex with pre-let7g miRNA and Lin28A
    • Complex: Terminal uridylyltransferase 4 and Protein lin-28 homolog A
      • Protein or peptide: Terminal uridylyltransferase 4
      • Protein or peptide: Protein lin-28 homolog A
    • Complex: pre-let7-g
      • RNA: pre-let7-g
  • Ligand: ZINC ION

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Supramolecule #1: Human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex w...

SupramoleculeName: Human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex with pre-let7g miRNA and Lin28A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Terminal uridylyltransferase 4 and Protein lin-28 homolog A

SupramoleculeName: Terminal uridylyltransferase 4 and Protein lin-28 homolog A
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: pre-let7-g

SupramoleculeName: pre-let7-g / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #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 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA uridylyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 185.433734 KDa
Recombinant expressionOrganism: Escherichia coli KRX (bacteria)
SequenceString: MEESKTLKSE NHEPKKNVIC EESKAVQVIG NQTLKARNDK SVKEIENSSP NRNSSKKNKQ NDICIEKTEV KSCKVNAANL PGPKDLGLV LRDQSHCKAK KFPNSPVKAE KATISQAKSE KATSLQAKAE KSPKSPNSVK AEKASSYQMK SEKVPSSPAE A EKGPSLLL ...String:
MEESKTLKSE NHEPKKNVIC EESKAVQVIG NQTLKARNDK SVKEIENSSP NRNSSKKNKQ NDICIEKTEV KSCKVNAANL PGPKDLGLV LRDQSHCKAK KFPNSPVKAE KATISQAKSE KATSLQAKAE KSPKSPNSVK AEKASSYQMK SEKVPSSPAE A EKGPSLLL KDMRQKTELQ QIGKKIPSSF TSVDKVNIEA VGGEKCALQN SPRSQKQQTC TDNTGDSDDS ASGIEDVSDD LS KMKNDES NKENSSEMDY LENATVIDES ALTPEQRLGL KQAEERLERD HIFRLEKRSP EYTNCRYLCK LCLIHIENIQ GAH KHIKEK RHKKNILEKQ EESELRSLPP PSPAHLAALS VAVIELAKEH GITDDDLRVR QEIVEEMSKV ITTFLPECSL RLYG SSLTR FALKSSDVNI DIKFPPKMNH PDLLIKVLGI LKKNVLYVDV ESDFHAKVPV VVCRDRKSGL LCRVSAGNDM ACLTT DLLT ALGKIEPVFI PLVLAFRYWA KLCYIDSQTD GGIPSYCFAL MVMFFLQQRK PPLLPCLLGS WIEGFDPKRM DDFQLK GIV EEKFVKWECN SSSATEKNSI AEENKAKADQ PKDDTKKTET DNQSNAMKEK HGKSPLALET PNRVSLGQLW LELLKFY TL DFALEEYVIC VRIQDILTRE NKNWPKRRIA IEDPFSVKRN VARSLNSQLV YEYVVERFRA AYRYFACPQT KGGNKSTV D FKKREKGKIS NKKPVKSNNM ATNGCILLGE TTEKINAERE QPVQCDEMDC TSQRCIIDNN NLLVNELDFA DHGQDSSSL STSKSSEIEP KLDKKQDDLA PSETCLKKEL SQCNCIDLSK SPDPDKSTGT DCRSNLETES SHQSVCTDTS ATSCNCKATE DASDLNDDD NLPTQELYYV FDKFILTSGK PPTIVCSICK KDGHSKNDCP EDFRKIDLKP LPPMTNRFRE ILDLVCKRCF D ELSPPCSE QHNREQILIG LEKFIQKEYD EKARLCLFGS SKNGFGFRDS DLDICMTLEG HENAEKLNCK EIIENLAKIL KR HPGLRNI LPITTAKVPI VKFEHRRSGL EGDISLYNTL AQHNTRMLAT YAAIDPRVQY LGYTMKVFAK RCDIGDASRG SLS SYAYIL MVLYFLQQRK PPVIPVLQEI FDGKQIPQRM VDGWNAFFFD KTEELKKRLP SLGKNTESLG ELWLGLLRFY TEEF DFKEY VISIRQKKLL TTFEKQWTSK CIAIEDPFDL NHNLGAGVSR KMTNFIMKAF INGRKLFGTP FYPLIGREAE YFFDS RVLT DGELAPNDRC CRVCGKIGHY MKDCPKRKSL LFRLKKKDSE EEKEGNEEEK DSRDVLDPRD LHDTRDFRDP RDLRCF ICG DAGHVRRECP EVKLARQRNS SVAAAQLVRN LVNAQQVAGS AQQQGDQSIR TRQSSECSES PSYSPQPQPF PQNSSQS AA ITQPSSQPGS QPKLGPPQQG AQPPHQVQMP LYNFPQSPPA QYSPMHNMGL LPMHPLQIPA PSWPIHGPVI HSAPGSAP S NIGLNDPSII FAQPAARPVA IPNTSHDGHW PRTVAPNSLV NSGAVGNSEP GFRGLTPPIP WEHAPRPHFP LVPASWPYG LHQNFMHQGN ARFQPNKPFY TQDRCATRRC RERCPHPPRG NVSE

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 / 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 #3: pre-let7-g

MacromoleculeName: pre-let7-g / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.287232 KDa
SequenceString:
GGUAGUAGUU UGUACAGUUU GAGGGUCUAU GAUACAACCC GGUACAGGAG AUAACUGUAC AGGCCACUG

GENBANK: GENBANK: AC092045.2

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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: GATAN K3 BIOQUANTUM (6k 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: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 186227
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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