- EMDB-53295: Ternary complex of translating ribosome, NAC and NMT1 -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: EMDB / ID: EMD-53295
Title
Ternary complex of translating ribosome, NAC and NMT1
Map data
Sample
Complex: Ternary complex of translating ribosome, NAC and NMT1
RNA: x 5 types
Protein or peptide: x 81 types
Ligand: x 6 types
Keywords
Translation / co-translational protein processing / RIBOSOME
Function / homology
Function and homology information
[histone H4]-N-methyl-L-lysine20 N-methyltransferase / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / myristoyltransferase activity / protein myristoylation / peptidyl-lysine N6-myristoyltransferase activity / CoA-dependent peptidyl-lysine N6-myristoyltransferase activity / Late Phase of HIV Life Cycle / N-terminal protein myristoylation / histone H4K20me methyltransferase activity ...[histone H4]-N-methyl-L-lysine20 N-methyltransferase / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / myristoyltransferase activity / protein myristoylation / peptidyl-lysine N6-myristoyltransferase activity / CoA-dependent peptidyl-lysine N6-myristoyltransferase activity / Late Phase of HIV Life Cycle / N-terminal protein myristoylation / histone H4K20me methyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / regulation of skeletal muscle fiber development / ketone metabolic process / positive regulation of skeletal muscle tissue growth / regulation of opsin-mediated signaling pathway / positive regulation of cell proliferation involved in heart morphogenesis / cardiac ventricle development / Activation, myristolyation of BID and translocation to mitochondria / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / heart trabecula morphogenesis / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / skeletal muscle tissue regeneration / protein-RNA complex assembly / S-adenosyl-L-methionine binding / protein localization to membrane / negative regulation of striated muscle cell apoptotic process / positive regulation of double-strand break repair via nonhomologous end joining / positive regulation of protein localization to mitochondrion / regulation of translation involved in cellular response to UV / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / laminin receptor activity / negative regulation of myoblast fusion / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / pericentric heterochromatin / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / ubiquitin ligase inhibitor activity / 90S preribosome / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of signal transduction by p53 class mediator / 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 / phagocytic cup / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / eNOS activation / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / ribosomal small subunit export from nucleus / rough endoplasmic reticulum / laminin binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of apoptotic signaling pathway / MDM2/MDM4 family protein binding / wound healing / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA damage response, signal transduction by p53 class mediator / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / striated muscle contraction / Maturation of DENV proteins / positive regulation of translation / small-subunit processome / cellular response to gamma radiation / Dengue Virus Genome Translation and Replication / spindle / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / mRNA 5'-UTR binding / rRNA processing / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / transcription coactivator binding / cytosolic ribosome / glucose homeostasis / large ribosomal subunit / Inactivation, recovery and regulation of the phototransduction cascade / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / spermatogenesis / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit 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 / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / NAC A/B domain superfamily ...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 / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / 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 / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / SET domain profile. / SET domain / SET domain superfamily / Ubiquitin-like protein FUBI / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L1, conserved site / Ribosomal protein L23 / Ribosomal protein L1 signature. / Ribosomal protein L2, archaeal-type / Ribosomal protein L1 / metallochaperone-like domain / TRASH domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L13e / Ribosomal L38e protein family / Ribosomal protein S21e / Ribosomal protein L38e superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / : / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L6e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Acyl-CoA N-acyltransferase / 40S Ribosomal protein S10 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Plectin/S10, N-terminal / Ribosomal protein L18/L18-A/B/e, conserved site / Plectin/S10 domain 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 / Transcription factor BTF3 / Glycylpeptide N-tetradecanoyltransferase 1 / Large ribosomal subunit protein eL8 / Nascent polypeptide-associated complex subunit alpha / Large ribosomal subunit protein eL37 Similarity search - Component
Biological species
Oryctolagus cuniculus (rabbit) / Homo sapiens (human)
Method
single particle reconstruction / cryo EM / Resolution: 2.8 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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi