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- EMDB-17086: Human terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre... -

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Basic information

Entry
Database: EMDB / ID: EMD-17086
TitleHuman terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 1
Map dataHuman terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 1
Sample
  • Complex: Human terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 1
    • 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 (71-MER) Let7g
      • RNA: RNA (71-MER) Let7g
  • Ligand: ZINC ION
KeywordsPolymerase / uridylation / RNA maturation and turnover control / RNA
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 / retrotransposon silencing by mRNA destabilization / uridylyltransferase activity / protein-RNA adaptor activity / RNA 3'-end processing / miRNA catabolic process / 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 / retrotransposon silencing by mRNA destabilization / uridylyltransferase activity / 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 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 / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain ...Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / 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: 3.82 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: Yi G / Ye M / Carrique L / El-Sagheer A / Brown T / Norbury CJ / Zhang P / Gilbert RJC
History
DepositionApr 8, 2023-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17086.png

Downloads & links

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Map

FileDownload / File: emd_17086.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 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 350 pix.
= 325.5 Å		0.93 Å/pix.
x 350 pix.
= 325.5 Å		0.93 Å/pix.
x 350 pix.
= 325.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0204
Minimum - Maximum-0.0019297703 - 2.2650478
Average (Standard dev.)0.0007129265 (±0.018243218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 325.5 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_17086_half_map_1.map
AnnotationHuman terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - 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 7 (TUT7/ZCCHC6) bound with pre-let7g...

Fileemd_17086_half_map_2.map
AnnotationHuman terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - 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 7 (TUT7/ZCCHC6) bound with pre...

EntireName: Human terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 1
Components
  • Complex: Human terminal uridylyltransferase 7 (TUT7/ZCCHC6) bound with pre-let7g miRNA and Lin28A - complex 1
    • 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 (71-MER) Let7g
      • RNA: RNA (71-MER) Let7g
  • 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 1
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-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: RNA (71-MER) Let7g

SupramoleculeName: RNA (71-MER) Let7g / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
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: 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: RNA (71-MER) Let7g

MacromoleculeName: RNA (71-MER) Let7g / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.858557 KDa
SequenceString:
GGUAGUAAUU UGUACAGUUU GAGGGUCUAU GAUACCACCC GGUACAGGAG AUAACUGUAC AGGCCACUGC U

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / 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: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 183972
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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