8ORJ | pdb_00008orj

Cryo-EM structure of human tRNA ligase RTCB in complex with human PYROXD1.

• PDB DOI: https://doi.org/10.2210/pdb8ORJ/pdb
• EM Map EMD-17127: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-14 Released: 2024-10-30 
• Deposition Author(s): Loeff, L., Kroupova, A., Asanovic, I., Boneberg, F., Pfleiderer, M.M., Ferdigg, A., Ackle, F., Martinez, J., Jinek, M.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanistic basis for PYROXD1-mediated protection of the human tRNA ligase complex against oxidative inactivation.

Loeff, L., Kroupova, A., Asanovic, I., Boneberg, F.M., Pfleiderer, M.M., Riermeier, L., Leitner, A., Ferdigg, A., Ackle, F., Martinez, J., Jinek, M.

(2025) Nat Struct Mol Biol 

• PubMed: 40069351 
• DOI: https://doi.org/10.1038/s41594-025-01516-6
• Primary Citation Related Structures: 
  8ORJ


• PubMed Abstract: 
  

  The metazoan tRNA ligase complex (tRNA-LC) has essential roles in tRNA biogenesis and unfolded protein response. Its catalytic subunit RTCB contains a conserved active-site cysteine that is susceptible to metal ion-induced oxidative inactivation. The flavin-containing oxidoreductase PYROXD1 preserves the activity of human tRNA-LC in a NAD(P)H-dependent manner, but its protective mechanism remains elusive. Here, we report a cryogenic electron microscopic structure of the human RTCB-PYROXD1 complex, revealing that PYROXD1 directly interacts with the catalytic center of RTCB through its carboxy-terminal tail. NAD(P)H binding and FAD reduction allosterically control PYROXD1 activity and RTCB recruitment, while reoxidation of PYROXD1 enables timed release of RTCB. PYROXD1 interaction is mutually exclusive with Archease-mediated RTCB guanylylation, and guanylylated RTCB is intrinsically protected from oxidative inactivation. Together, these findings provide a mechanistic framework for the protective function of PYROXD1 that maintains the activity of the tRNA-LC under aerobic conditions.

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Organizational Affiliation: 
• Department of Biochemistry, University of Zurich, Zurich, Switzerland.
Centre for Targeted Protein Degradation, University of Dundee, Dundee, UK.
Max Perutz Labs, Medical University of Vienna, Vienna BioCenter, Vienna, Austria.
Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zurich, Switzerland.
Department of Biochemistry, University of Zurich, Zurich, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 113.07 kDa 
• Atom Count: 6,930 
• Modeled Residue Count: 882 
• Deposited Residue Count: 1,010 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-splicing ligase RtcB homolog	A	508	Homo sapiens	Mutation(s): 0  Gene Names: RTCB, C22orf28, HSPC117 EC: 6.5.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3I0 (Homo sapiens) Explore Q9Y3I0  Go to UniProtKB:  Q9Y3I0
PHAROS:  Q9Y3I0 GTEx:  ENSG00000100220

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1	B	502	Homo sapiens	Mutation(s): 0  Gene Names: PYROXD1 EC: 1.8.1 (PDB Primary Data), 1.6.99.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WU10 (Homo sapiens) Explore Q8WU10  Go to UniProtKB:  Q8WU10
PHAROS:  Q8WU10 GTEx:  ENSG00000121350

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FDA (Subject of Investigation/LOI)	F [auth B]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C27 H35 N9 O15 P2 YPZRHBJKEMOYQH-UYBVJOGSSA-N
NAD (Subject of Investigation/LOI)	E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
MG (Subject of Investigation/LOI)	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.3.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Loeff, L., Kroupova, A., Asanovic, I., Boneberg, F., Pfleiderer, M.M., Ferdigg, A., Ackle, F., Martinez, J., Jinek, M.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A_182567

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release
  
• Version 1.1: 2025-05-07
  Changes: Data collection, Database references