N-terminal domain of CGI-99

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report

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Molecular architecture of the human tRNA ligase complex.

Kroupova, A.Ackle, F.Asanovic, I.Weitzer, S.Boneberg, F.M.Faini, M.Leitner, A.Chui, A.Aebersold, R.Martinez, J.Jinek, M.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.71656
  • Primary Citation of Related Structures:  
    7P3A, 7P3B

  • PubMed Abstract: 

    RtcB enzymes are RNA ligases that play essential roles in tRNA splicing, unfolded protein response, and RNA repair. In metazoa, RtcB functions as part of a five-subunit tRNA ligase complex (tRNA-LC) along with Ddx1, Cgi-99, Fam98B, and Ashwin. The human tRNA-LC or its individual subunits have been implicated in additional cellular processes including microRNA maturation, viral replication, DNA double-strand break repair, and mRNA transport. Here, we present a biochemical analysis of the inter-subunit interactions within the human tRNA-LC along with crystal structures of the catalytic subunit RTCB and the N-terminal domain of CGI-99. We show that the core of the human tRNA-LC is assembled from RTCB and the C-terminal alpha-helical regions of DDX1, CGI-99, and FAM98B, all of which are required for complex integrity. The N-terminal domain of CGI-99 displays structural homology to calponin-homology domains, and CGI-99 and FAM98B associate via their N-terminal domains to form a stable subcomplex. The crystal structure of GMP-bound RTCB reveals divalent metal coordination geometry in the active site, providing insights into its catalytic mechanism. Collectively, these findings shed light on the molecular architecture and mechanism of the human tRNA ligase complex and provide a structural framework for understanding its functions in cellular RNA metabolism.

  • Organizational Affiliation

    Department of Biochemistry, University of Zurich, Zurich, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA transcription, translation and transport factor protein
A, B
103Homo sapiensMutation(s): 0 
Gene Names: RTRAFC14orf166CGI-99
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y224 (Homo sapiens)
Explore Q9Y224 
Go to UniProtKB:  Q9Y224
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y224
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MPD

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
C6 H14 O2
Query on IPA

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
H [auth B]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
H [auth B],
I [auth B],
J [auth B]
C3 H8 O
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.714α = 90
b = 91.714β = 90
c = 52.942γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
University of ZurichSwitzerlandFK-18-033
Swiss National Science FoundationSwitzerlandNational Competence Center for Research (NCCR) RNA & Disease

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release