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Structure paper

TitleTranslation initiation by the Kozak mRNA sequence is based on a conformational readout on the ribosome.
Journal, issue, pagesNat Commun, Year 2026
Publish dateJul 8, 2026
AuthorsOttilie von Loeffelholz / Charles Barchet / Samuel Holvec / Aida Abou Ramadan / Cristina Protuc / Anne Maglott-Roth / S Nimali T de Silva / Isabelle Hazemann / Bruno P Klaholz /
PubMed AbstractThe recognition mechanism of Kozak mRNA, typically comprising purines in the -3 and +4 positions flanking the AUG start codon, has remained enigmatic for decades. To address this fundamental function ...The recognition mechanism of Kozak mRNA, typically comprising purines in the -3 and +4 positions flanking the AUG start codon, has remained enigmatic for decades. To address this fundamental function in eukaryotes during translation initiation, we analysed several cryo-EM structures of human 48S preinitiation complexes with mRNA sequences differing in Kozak activity revealing distinct modes of recognition. The pre-codon triplet forms a fan-like intercalation into the 18S ribosomal RNA (rRNA), while a -3 pyrimidine destabilizes ternary complex positioning. Specificity towards the +4 purine is achieved beyond a single residue recognition by mutual conformational adaptations of eIF1A, mRNA and rRNA that involve the insertion of a reading head in which decoding residue A1825 (rRNA) stacks with the A-site codon to stabilize the fully accommodated state. Hence, instead of relying on base pairing as in bacteria, the specific recognition of the Kozak sequence on eukaryotic ribosomes is based on an induced-fit mechanism that triggers a conformational readout of the mRNA.
External linksNat Commun / PubMed:42420270
MethodsEM (single particle)
Resolution2.78 - 3.84 Å
Structure data

EMDB-56980: focused refined map; 40S head with TC from human 48S PIC on mRNA (non-Kozak)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-56981: consensus map; human 48S PIC on Kozak mRNA with eIF1A W70A mutant
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-56982: focused refined map; 40S body with eIF1A from human 48S PIC with eIF1A W70A mutant on Kozak mRNA
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-56983: focused refined map; 40S head with TC from human 48S PIC with eIF1A W70A mutant on Kozak mRNA
Method: EM (single particle) / Resolution: 3.2 Å

57004

28zu

EMDB-57004, PDB-28zu:
human 48S PIC with Kozak mRNA and eIF1A W70A mutant
Method: EM (single particle) / Resolution: 3.2 Å

57005

28zv

EMDB-57005, PDB-28zv:
human 48S PIC with mRNA (non-Kozak)
Method: EM (single particle) / Resolution: 2.9 Å

57009

28zx

EMDB-57009, PDB-28zx:
human 48S PIC with mRNA (Kozak_1)
Method: EM (single particle) / Resolution: 2.8 Å

57010

28zy

EMDB-57010, PDB-28zy:
human 48S PIC with mRNA (Kozak_2)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-57011: focused refined map; 40S body with eIF1A from human 48S PIC on mRNA (non-Kozak)
Method: EM (single particle) / Resolution: 2.95 Å

EMDB-57012: consensus map; human 48S PIC on mRNA (non-Kozak)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-57013: focused refined map; human eIF3 in 48S PIC on Kozak mRNA (Kozak_2)
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-57014: focused refined map; 40S head with TC from human 48S PIC on Kozak mRNA (Kozak_2)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-57015: focused refined map; 40S body with eIF1A from human 48S PIC on Kozak mRNA (Kozak_2)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-57016: consensus map; human 48S PIC on Kozak mRNA (Kozak_2)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-57017: focused refined map; map for 40S body from human 48S PIC on Kozak mRNA (Kozak_1)
Method: EM (single particle) / Resolution: 2.78 Å

EMDB-57018: focused refined map; 40S head with TC from human 48S PIC on Kozak mRNA (Kozak_1)
Method: EM (single particle) / Resolution: 2.85 Å

EMDB-57019: focused refined map; human eIF3 in 48S PIC on Kozak mRNA (Kozak_1)
Method: EM (single particle) / Resolution: 3.84 Å

EMDB-57020: consensus map; human 48S PIC on Kozak mRNA (Kozak_1)
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-K:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM

ChemComp-MET:
METHIONINE

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
  • homo (humans)
KeywordsRIBOSOME / translation initiation / 48S PIC / human / Kozak sequence

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