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Yorodumi- EMDB-17084: Structure of human terminal uridylyltransferase 7 (hTUT7/ZCCHC6) ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17084 | |||||||||
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Title | Structure of human terminal uridylyltransferase 7 (hTUT7/ZCCHC6) bound with pre-let7g miRNA and UTPalphaS | |||||||||
Map data | Human terminal uridylyltransferase 7 (TUT7, ZCCHC6) in complex with pre-let7g miRNA | |||||||||
Sample |
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Keywords | Polymerase / uridylation / RNA maturation and turnover control / RNA | |||||||||
Function / homology | Function and homology information polyuridylation-dependent mRNA catabolic process / retrotransposon silencing by mRNA destabilization / uridylyltransferase activity / RNA 3'-end processing / 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 / retrotransposon silencing by mRNA destabilization / uridylyltransferase activity / RNA 3'-end processing / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.76 Å | |||||||||
Authors | Yi G / Ye M / Gilbert RJ | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2024 Title: Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs Authors: Yi G / Ye M / Carrique L / El-Sagheer A / Brown T / Norbury CJ / Zhang P / Gilbert RJC | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17084.map.gz | 77.8 MB | EMDB map data format | |
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Header (meta data) | emd-17084-v30.xml emd-17084.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17084_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_17084.png | 85.3 KB | ||
Filedesc metadata | emd-17084.cif.gz | 6.7 KB | ||
Others | emd_17084_half_map_1.map.gz emd_17084_half_map_2.map.gz | 77.7 MB 77.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17084 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17084 | HTTPS FTP |
-Validation report
Summary document | emd_17084_validation.pdf.gz | 746.2 KB | Display | EMDB validaton report |
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Full document | emd_17084_full_validation.pdf.gz | 745.7 KB | Display | |
Data in XML | emd_17084_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | emd_17084_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17084 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17084 | HTTPS FTP |
-Related structure data
Related structure data | 8oppMC 8oefC 8opsC 8ostC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17084.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Human terminal uridylyltransferase 7 (TUT7, ZCCHC6) in complex with pre-let7g miRNA | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.932 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Human terminal uridylyltransferase 7 (TUT7, ZCCHC6) in complex...
File | emd_17084_half_map_1.map | ||||||||||||
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Annotation | Human terminal uridylyltransferase 7 (TUT7, ZCCHC6) in complex with pre-let7g miRNA, half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Human terminal uridylyltransferase 7 (TUT7, ZCCHC6) in complex...
File | emd_17084_half_map_2.map | ||||||||||||
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Annotation | Human terminal uridylyltransferase 7 (TUT7, ZCCHC6) in complex with pre-let7g miRNA, half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human terminal urildylyltransferase 7 (TUT7/ZCCHC6) bound with pr...
Entire | Name: human terminal urildylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA |
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Components |
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-Supramolecule #1: human terminal urildylyltransferase 7 (TUT7/ZCCHC6) bound with pr...
Supramolecule | Name: 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
Supramolecule | Name: Terminal uridylyltransferase 7 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: RNA (25-MER)
Supramolecule | Name: RNA (25-MER) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Terminal uridylyltransferase 7
Macromolecule | Name: Terminal uridylyltransferase 7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA uridylyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 171.493766 KDa |
Recombinant expression | Organism: Escherichia coli KRX (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: RNA (25-MER)
Macromolecule | Name: RNA (25-MER) / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.007763 KDa |
Sequence | String: UGAGGUAGUA GUGCCACUGC CUUGC |
-Macromolecule #3: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-...
Macromolecule | Name: [[(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 |
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Molecular weight | Theoretical: 500.207 Da |
Chemical component information | ChemComp-P5E: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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 |