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- PDB-8ost: Structure of human terminal uridylyltransferase 4 (TUT4, ZCCHC11)... -

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Basic information

Entry
Database: PDB / ID: 8ost
TitleStructure of human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex with pre-let7g miRNA and Lin28A
Components
  • Protein lin-28 homolog A
  • Terminal uridylyltransferase 4
  • pre-let7-g
KeywordsCELL CYCLE / Polymerase / 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 / 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
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 / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Cold shock domain ...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 / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / 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
: / RNA / RNA (> 10) / Terminal uridylyltransferase 4 / Protein lin-28 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsGilbert, R.J. / Yi, G. / Ye, M.
Funding support United Kingdom, 1items
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: Ye, G. / Yi, M. / Carrique, L. / El-Sagheer, A. / Brown, T. / Norbury, C.J. / Zhang, P. / Gilbert, R.J.
History
DepositionApr 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terminal uridylyltransferase 4
B: Protein lin-28 homolog A
C: pre-let7-g
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,6315
Polymers230,5003
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-15 kcal/mol
Surface area36420 Å2
MethodPISA

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Components

#1: Protein Terminal uridylyltransferase 4 / TUTase 4 / Zinc finger CCHC domain-containing protein 11


Mass: 185433.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUT4, KIAA0191, ZCCHC11 / Production host: Escherichia coli KRX (bacteria) / References: UniProt: Q5TAX3, RNA uridylyltransferase
#2: Protein Protein lin-28 homolog A / Lin-28A / Zinc finger CCHC domain-containing protein 1


Mass: 22778.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIN28A, CSDD1, LIN28, ZCCHC1 / Production host: Escherichia coli KRX (bacteria) / References: UniProt: Q9H9Z2
#3: RNA chain pre-let7-g


Mass: 22287.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 15281257
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex with pre-let7g miRNA and Lin28ACOMPLEX#1-#30MULTIPLE SOURCES
2Terminal uridylyltransferase 4 and Protein lin-28 homolog ACOMPLEX#1-#21RECOMBINANT
3pre-let7-gCOMPLEX#31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
22Escherichia coli KRX (bacteria)1452720KRX
33Synthetic construct (others)32630
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 186227 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025179
ELECTRON MICROSCOPYf_angle_d0.5097358
ELECTRON MICROSCOPYf_dihedral_angle_d18.1621306
ELECTRON MICROSCOPYf_chiral_restr0.037890
ELECTRON MICROSCOPYf_plane_restr0.006672

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