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- EMDB-17164: Structure of human terminal uridylyltransferase 4 (TUT4, ZCCHC11)... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Structure of human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex with pre-let7g miRNA and Lin28A | |||||||||
![]() | Human terminal uridylyltransferase 4 (TUT4; ZCCHC11) bound with pre-let7-g miRNA and Lin28A (equivalent to TUT7 complex 1) | |||||||||
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![]() | Polymerase / uridylation / RNA maturation and turnover control / RNA / CELL CYCLE | |||||||||
Function / homology | ![]() 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 / retrotransposon silencing by mRNA destabilization / protein-RNA adaptor activity / RNA 3'-end processing / miRNA catabolic process / 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 / retrotransposon silencing by mRNA destabilization / protein-RNA adaptor activity / RNA 3'-end processing / miRNA catabolic process / 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 / positive regulation of cytoplasmic translation / pre-miRNA processing / sequence-specific mRNA binding / oocyte maturation / miRNA binding / stem cell population maintenance / germ cell development / Zygotic genome activation (ZGA) / 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 / RNA binding / extracellular space / zinc ion binding / extracellular exosome / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.69 Å | |||||||||
![]() | Gilbert RJ / Yi G / Ye M | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs Authors: Ye G / Yi M / Carrique L / El-Sagheer A / Brown T / Norbury CJ / Zhang P / Gilbert RJ | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 203.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.7 KB 18.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.7 KB | Display | ![]() |
Images | ![]() | 28.2 KB | ||
Filedesc metadata | ![]() | 7 KB | ||
Others | ![]() ![]() | 200.3 MB 200.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 828.6 KB | Display | ![]() |
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Full document | ![]() | 828.2 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ostMC ![]() 8oefC ![]() 8oppC ![]() 8opsC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | Human terminal uridylyltransferase 4 (TUT4; ZCCHC11) bound with pre-let7-g miRNA and Lin28A (equivalent to TUT7 complex 1) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Human terminal uridylyltransferase 4 (TUT4; ZCCHC11) bound with...
File | emd_17164_half_map_1.map | ||||||||||||
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Annotation | Human terminal uridylyltransferase 4 (TUT4; ZCCHC11) bound with pre-let7-g miRNA and Lin28A (equivalent to TUT7 complex 1) - half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Human terminal uridylyltransferase 4 (TUT4; ZCCHC11) bound with...
File | emd_17164_half_map_2.map | ||||||||||||
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Annotation | Human terminal uridylyltransferase 4 (TUT4; ZCCHC11) bound with pre-let7-g miRNA and Lin28A (equivalent to TUT7 complex 1) - half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex w...
Entire | Name: Human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex with pre-let7g miRNA and Lin28A |
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Components |
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-Supramolecule #1: Human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex w...
Supramolecule | Name: 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
Supramolecule | Name: Terminal uridylyltransferase 4 and Protein lin-28 homolog A type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: pre-let7-g
Supramolecule | Name: pre-let7-g / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Terminal uridylyltransferase 4
Macromolecule | Name: Terminal uridylyltransferase 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA uridylyltransferase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 185.433734 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: Protein lin-28 homolog A
Macromolecule | Name: Protein lin-28 homolog A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 22.778975 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: pre-let7-g
Macromolecule | Name: pre-let7-g / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 22.287232 KDa |
Sequence | String: GGUAGUAGUU UGUACAGUUU GAGGGUCUAU GAUACAACCC GGUACAGGAG AUAACUGUAC AGGCCACUG GENBANK: GENBANK: AC092045.2 |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 |