- EMDB-53296: Quaternary complex of a translating ribosome, NAC, NMT1, and NatA -
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Basic information
Entry
Database: EMDB / ID: EMD-53296
Title
Quaternary complex of a translating ribosome, NAC, NMT1, and NatA
Map data
Primary map
Sample
Complex: Quaternary complex of translating ribosome, NAC, NMT1 and NatA
RNA: x 5 types
Protein or peptide: x 83 types
Protein or peptide: x 1 types
Ligand: x 7 types
Keywords
Translation / co-translational protein processing / RIBOSOME
Function / homology
Function and homology information
negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / negative regulation of striated muscle cell apoptotic process / protein-N-terminal-glutamate acetyltransferase activity / regulation of skeletal muscle fiber development / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal protein amino acid acetylation / myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / negative regulation of striated muscle cell apoptotic process / protein-N-terminal-glutamate acetyltransferase activity / regulation of skeletal muscle fiber development / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal protein amino acid acetylation / myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / positive regulation of cell proliferation involved in heart morphogenesis / [histone H4]-lysine20 N-methyltransferase / NatA complex / Late Phase of HIV Life Cycle / positive regulation of skeletal muscle tissue growth / protein N-terminal-serine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / ketone metabolic process / histone H4K20 methyltransferase activity / regulation of opsin-mediated signaling pathway / protein-N-terminal amino-acid acetyltransferase activity / internal protein amino acid acetylation / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / cardiac ventricle development / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of protein localization to mitochondrion / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / heart trabecula morphogenesis / N-acetyltransferase activity / skeletal muscle tissue regeneration / acetyltransferase activator activity / ribosomal subunit / S-adenosyl-L-methionine binding / protein localization to membrane / protein acetylation / positive regulation of double-strand break repair via nonhomologous end joining / laminin receptor activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ubiquitin ligase inhibitor activity / chromosome organization / Viral mRNA Translation / positive regulation of signal transduction by p53 class mediator / 90S preribosome / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / pericentric heterochromatin / phagocytic cup / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / eNOS activation / laminin binding / rough endoplasmic reticulum / translation regulator activity / ribosomal small subunit export from nucleus / gastrulation / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / MDM2/MDM4 family protein binding / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / wound healing / small-subunit processome / spindle / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of canonical Wnt signaling pathway / rhythmic process / Inactivation, recovery and regulation of the phototransduction cascade / heparin binding / regulation of translation / protein transport / large ribosomal subunit / ribosome binding / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / angiogenesis Similarity search - Function
Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Nascent polypeptide-associated complex subunit alpha / N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / N-acetyltransferase Ard1-like ...Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Nascent polypeptide-associated complex subunit alpha / N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / N-acetyltransferase Ard1-like / Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / NAC A/B domain superfamily / NAC domain / NAC A/B domain profile. / NAC / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / : / : / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 40S ribosomal protein SA / Acetyltransferase (GNAT) family / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Tetratricopeptide repeat / Ribosomal protein L30e / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / Ribosomal L15/L27a, N-terminal / 50S ribosomal protein L10, insertion domain superfamily / SET domain / SET domain profile. / SET domain superfamily / SET domain / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / metallochaperone-like domain / Ribosomal protein L1, conserved site / TRASH domain / Ribosomal protein L1 signature. / Ribosomal protein L1 / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S12e / Ribosomal protein L27e, conserved site / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / TPR repeat region circular profile. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L38e / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L38e superfamily / Ribosomal protein L1p/L10e family / Ribosomal L38e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L44e signature. Similarity search - Domain/homology
Small ribosomal subunit protein eS32 / 40S ribosomal protein S26 / Large ribosomal subunit protein eL28 / Ribosomal protein L32 / 60S ribosomal protein L36a-like / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Ribosomal protein L18 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL24 ...Small ribosomal subunit protein eS32 / 40S ribosomal protein S26 / Large ribosomal subunit protein eL28 / Ribosomal protein L32 / 60S ribosomal protein L36a-like / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Ribosomal protein L18 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein uS11 / 40S ribosomal protein S24 / Large ribosomal subunit protein uL14 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Ribosomal protein L19 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein eL20 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS5 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL18 / Transcription factor BTF3 / Glycylpeptide N-tetradecanoyltransferase 1 / N-alpha-acetyltransferase 10 / Large ribosomal subunit protein eL8 / Nascent polypeptide-associated complex subunit alpha / N-alpha-acetyltransferase 15, NatA auxiliary subunit / Large ribosomal subunit protein eL37 Similarity search - Component
Biological species
Oryctolagus cuniculus (rabbit) / Homo sapiens (human)
Method
single particle reconstruction / cryo EM / Resolution: 3.43 Å
Journal: Mol Cell / Year: 2025 Title: Mechanism of cotranslational protein N-myristoylation in human cells. Authors: Martin Gamerdinger / Blanca Echeverria / Alfred M Lentzsch / Nicolas Burg / Ziyi Fan / Mateusz Jaskolowski / Alain Scaiola / Selina Piening / Shu-Ou Shan / Nenad Ban / Elke Deuerling / Abstract: N-myristoyltransferases (NMTs) cotranslationally transfer the fatty acid myristic acid to the N terminus of newly synthesized proteins, regulating their function and cellular localization. These ...N-myristoyltransferases (NMTs) cotranslationally transfer the fatty acid myristic acid to the N terminus of newly synthesized proteins, regulating their function and cellular localization. These enzymes are important drug targets for the treatment of cancer and viral infections. N-myristoylation of nascent proteins occurs specifically on N-terminal glycine residues after the excision of the initiator methionine by methionine aminopeptidases (METAPs). How NMTs interact with ribosomes and gain timely and specific access to their substrates remains unknown. Here, we show that human NMT1 exchanges with METAP1 at the ribosomal tunnel exit to form an active cotranslational complex together with the nascent polypeptide-associated complex (NAC). NMT1 binding is sequence selective and specifically triggered by methionine excision, which exposes the N-myristoylation motif in the nascent chain. The revealed mode of interaction of NMT1 with NAC and the methionine-cleaved nascent protein elucidates how a specific subset of proteins can be efficiently N-myristoylated in human cells.
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