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Structure paper

TitleStructural mechanism of mRNA decoding by mammalian GTPase GTPBP1.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Page 148, Year 2025
Publish dateDec 5, 2025
AuthorsDenis Susorov / Anna Miścicka / Dmitrij Golovenko / Anna B Loveland / Alexandra Zinoviev / Tatyana V Pestova / Andrei A Korostelev /
PubMed AbstractGTP-binding protein 1 (GTPBP1) is a widespread translational GTPase closely related to elongation factor eEF1A. The loss of GTPBP1 leads to neurodevelopmental and neurodegenerative disorders in ...GTP-binding protein 1 (GTPBP1) is a widespread translational GTPase closely related to elongation factor eEF1A. The loss of GTPBP1 leads to neurodevelopmental and neurodegenerative disorders in animals. Although linked to translation and quality control mechanisms, GTPBP1 molecular functions remain largely obscure. Similarly to eEF1A, GTPBP1 delivers aminoacyl-tRNA to the ribosome, but the ensuing GTPBP1-mediated elongation is slow. Here, using cryo-EM of mammalian 80S ribosomal complexes bound to GTPBP1 and aa-tRNA with GTP or the non-hydrolysable analog GDPCP, we show that the distinct GTPBP1 architecture and interactions with tRNA underlie slow GTPBP1 dissociation after GTP hydrolysis, resulting in delayed tRNA accommodation. Slow dissociation correlates with an extended proofreading stage and higher accuracy of GTPBP1-mediated decoding, potentially allowing GTPBP1 to elicit its putative quality control functions. GTPBP1 visualization provides the foundation for mapping and elucidating GTPBP1 mutations associated with human diseases.
External linksNat Commun / PubMed:41350250 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 3.1 Å
Structure data

73297

9ypg

EMDB-73297, PDB-9ypg:
GTPBP1*GCP*Phe-tRNA*ribosome in the GTPase activation-like state, Structure III
Method: EM (single particle) / Resolution: 3.0 Å

73302

9ypo

EMDB-73302, PDB-9ypo:
GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIa
Method: EM (single particle) / Resolution: 3.0 Å

73307

9yps

EMDB-73307, PDB-9yps:
GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIb
Method: EM (single particle) / Resolution: 3.0 Å

73308

9ypt

EMDB-73308, PDB-9ypt:
GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIc
Method: EM (single particle) / Resolution: 3.1 Å

73310

9ypv

EMDB-73310, PDB-9ypv:
GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IId
Method: EM (single particle) / Resolution: 3.0 Å

73311

9ypw

EMDB-73311, PDB-9ypw:
GTPBP1*GDP*Phe-tRNA*ribosome in the post-GTP hydrolysis state, Structure IV
Method: EM (single particle) / Resolution: 2.9 Å

73314

9ypy

EMDB-73314, PDB-9ypy:
Ribosome with accommodated A-site tRNA, Structure V
Method: EM (single particle) / Resolution: 3.0 Å

73315

9ypz

EMDB-73315, PDB-9ypz:
Vacant ribosome with P-site tRNA, substate 1, Structure Ia
Method: EM (single particle) / Resolution: 2.9 Å

73316

9yq0

EMDB-73316, PDB-9yq0:
Vacant ribosome with P-site tRNA, substate 2, Structure Ib
Method: EM (single particle) / Resolution: 2.9 Å

73317

9yq1

EMDB-73317, PDB-9yq1:
Vacant ribosome with P-site tRNA, substate 3, Structure Ic
Method: EM (single particle) / Resolution: 2.9 Å

Chemicals

ChemComp-SPD:
SPERMIDINE

ChemComp-ZN:
Unknown entry

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

ChemComp-PHE:
PHENYLALANINE

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-MET:
METHIONINE

ChemComp-K:
Unknown entry

ChemComp-GCP:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-PCP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

Source
  • oryctolagus cuniculus (rabbit)
  • saccharomyces cerevisiae (brewer's yeast)
  • homo sapiens (human)
KeywordsRIBOSOME / GTPBP1 / tRNA / GCP / complex

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