9I8V | pdb_00009i8v

Cryo-EM structure of the Danio rerio tRNA ligase complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history


Literature

Structural and biochemical characterization of the 3'-5' tRNA splicing ligases.

Chamera, S.Zajko, W.Czarnocki-Cieciura, M.Jaciuk, M.Koziej, L.Nowak, J.Wycisk, K.Sroka, M.Chramiec-Glabik, A.Smietanski, M.Golebiowski, F.Warminski, M.Jemielity, J.Glatt, S.Nowotny, M.

(2025) J Biological Chem 301: 108506-108506

  • DOI: https://doi.org/10.1016/j.jbc.2025.108506
  • Primary Citation of Related Structures:  
    9I8V

  • PubMed Abstract: 

    In archaea and metazoa, tRNA exons are ligated by the RNA ligases RtcB and RTCB, respectively. The metazoan RTCB forms a stable complex with four additional subunits, DDX1, FAM98B, CGI99 and ASHWIN. The role and assembly of these four components remain elusive. Furthermore, we lack structural information of how RNA substrates are recognized by 3'-5' tRNA ligases. Here, we use thiol-based chemical cross-linking to confirm the involvement of specific residues of RtcB in RNA binding and we present a cryo-electron microscopy structure of the purified five-subunit D. rerio tRNA ligase complex. The structure implies that the DDX1 helicase module is mobile and can modulate the activity of RTCB. Taken together, the presented results enhance our mechanistic understanding of RNA binding by 3'-5' tRNA splicing ligases and architecture of the metazoan tRNA ligase complex.


  • Organizational Affiliation
    • Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicaseA [auth B]48Danio rerioMutation(s): 0 
Gene Names: ddx1si:ch211-214k9.2si:dkey-161f12.1
EC: 3.6.4.13
UniProt
Find proteins for F1R2L8 (Danio rerio)
Explore F1R2L8 
Go to UniProtKB:  F1R2L8
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UniProt GroupF1R2L8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-splicing ligase RtcB homologB [auth C]519Danio rerioMutation(s): 0 
Gene Names: rtcbzgc:76871
EC: 6.5.1.8
UniProt
Find proteins for Q6NZS4 (Danio rerio)
Explore Q6NZS4 
Go to UniProtKB:  Q6NZS4
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UniProt GroupQ6NZS4
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Family with sequence similarity 98, member BC [auth D]296Danio rerioMutation(s): 0 
Gene Names: fam98bzgc:158382
UniProt
Find proteins for A0PJS3 (Danio rerio)
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UniProt GroupA0PJS3
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA transcription, translation and transport factor proteinD [auth E]242Danio rerioMutation(s): 1 
Gene Names: rtrafzgc:56576
UniProt
Find proteins for Q7ZUH1 (Danio rerio)
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UniProt GroupQ7ZUH1
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
AshwinE [auth F]83Danio rerioMutation(s): 0 
Gene Names: im:6907446si:dkeyp-118h3.6
UniProt
Find proteins for Q32LR5 (Danio rerio)
Explore Q32LR5 
Go to UniProtKB:  Q32LR5
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UniProt GroupQ32LR5
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2019/33/B/NZ1/02839

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Data collection, Database references