8BTX

Structure of human Archease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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


Literature

Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease.

Gerber, J.L.Morales Guzman, S.I.Worf, L.Hubbe, P.Kopp, J.Peschek, J.

(2024) Nat Commun 15: 2378-2378

  • DOI: https://doi.org/10.1038/s41467-024-46568-2
  • Primary Citation of Related Structures:  
    8BTT, 8BTX, 8ODO, 8ODP

  • PubMed Abstract: 

    RNA ligases of the RTCB-type play an essential role in tRNA splicing, the unfolded protein response and RNA repair. RTCB is the catalytic subunit of the pentameric human tRNA ligase complex. RNA ligation by the tRNA ligase complex requires GTP-dependent activation of RTCB. This active site guanylylation reaction relies on the activation factor Archease. The mechanistic interplay between both proteins has remained unknown. Here, we report a biochemical and structural analysis of the human RTCB-Archease complex in the pre- and post-activation state. Archease reaches into the active site of RTCB and promotes the formation of a covalent RTCB-GMP intermediate through coordination of GTP and metal ions. During the activation reaction, Archease prevents futile RNA substrate binding to RTCB. Moreover, monomer structures of Archease and RTCB reveal additional states within the RNA ligation mechanism. Taken together, we present structural snapshots along the reaction cycle of the human tRNA ligase.


  • Organizational Affiliation

    Heidelberg University, Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein archease183Homo sapiensMutation(s): 0 
Gene Names: ZBTB8OS
UniProt & NIH Common Fund Data Resources
Find proteins for A8K0B5 (Homo sapiens)
Explore A8K0B5 
Go to UniProtKB:  A8K0B5
GTEx:  ENSG00000176261 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8K0B5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 42 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.981α = 90
b = 79.981β = 90
c = 65.164γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany442512666

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 1.1: 2024-04-17
    Changes: Database references