negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / regulation of skeletal muscle fiber development / negative regulation of striated muscle cell apoptotic process / positive regulation of cell proliferation involved in heart morphogenesis / positive regulation of skeletal muscle tissue growth / cardiac ventricle development / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / N-terminal protein amino acid modification ...negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / regulation of skeletal muscle fiber development / negative regulation of striated muscle cell apoptotic process / positive regulation of cell proliferation involved in heart morphogenesis / positive regulation of skeletal muscle tissue growth / cardiac ventricle development / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / N-terminal protein amino acid modification / hemostasis / peptidyl-methionine modification / skeletal muscle tissue regeneration / glucose 6-phosphate metabolic process / initiator methionyl aminopeptidase activity / heart trabecula morphogenesis / methionyl aminopeptidase / carbohydrate derivative binding / metalloexopeptidase activity / Gluconeogenesis / negative regulation of RNA splicing / monosaccharide binding / Glycolysis / erythrocyte homeostasis / ciliary membrane / regulation of G1 to G0 transition / laminin receptor activity / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / positive regulation of immunoglobulin production / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / organelle membrane / mammalian oogenesis stage / G1 to G0 transition / response to testosterone / activation-induced cell death of T cells / Peptide chain elongation / metalloaminopeptidase activity / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / phagocytic cup / Eukaryotic Translation Termination / humoral immune response / ubiquitin ligase inhibitor activity / protein maturation / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / mesoderm formation / Viral mRNA Translation / response to immobilization stress / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / T cell proliferation involved in immune response / protein-RNA complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / erythrocyte development / negative regulation of ubiquitin-dependent protein catabolic process / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / cellular response to actinomycin D / ribosomal small subunit export from nucleus / aminopeptidase activity / response to cadmium ion / cytosolic ribosome / laminin binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / response to muscle stretch / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / 90S preribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / positive regulation of endothelial cell migration / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / positive regulation of apoptotic signaling pathway / cellular response to leukemia inhibitory factor / cytokine activity / maturation of SSU-rRNA / gluconeogenesis / response to progesterone / small-subunit processome / positive regulation of translation / glycolytic process / TP53 Regulates Metabolic Genes / protein kinase C binding / growth factor activity Similarity search - Function
Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / Nascent polypeptide-associated complex subunit alpha / NAC A/B domain superfamily / NAC domain / NAC A/B domain profile. / NAC / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / Zinc finger C6H2-type profile. ...Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / Nascent polypeptide-associated complex subunit alpha / NAC A/B domain superfamily / NAC domain / NAC A/B domain profile. / NAC / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / Zinc finger C6H2-type profile. / MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / SIS domain superfamily / Peptidase M24, methionine aminopeptidase / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Peptidase M24 / Metallopeptidase family M24 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Creatinase/aminopeptidase-like / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / : / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / : / Ribosomal protein L23 / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / Ribosomal protein S26e signature. / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / metallochaperone-like domain / Ribosomal protein S12e signature. / TRASH domain / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L1, conserved site / S27a-like superfamily / 40S Ribosomal protein S10 / Ribosomal protein L1 signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L1 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / : / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein L44e signature. Similarity search - Domain/homology
Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL20 / Ubiquitin-60S ribosomal protein L40 / 40S ribosomal protein S26 / Transcription factor BTF3 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / 60S ribosomal protein L8 ...Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL20 / Ubiquitin-60S ribosomal protein L40 / 40S ribosomal protein S26 / Transcription factor BTF3 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / 60S ribosomal protein L8 / Ribosomal protein L18 / 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 uL18 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL15 / 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 / 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 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 eL39 / Large ribosomal subunit protein eL36 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL19 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS5 / Glucose-6-phosphate isomerase / Methionine aminopeptidase 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: 2.9 Å
Journal: Science / Year: 2023 Title: NAC controls cotranslational N-terminal methionine excision in eukaryotes. Authors: Martin Gamerdinger / Min Jia / Renate Schloemer / Laurenz Rabl / Mateusz Jaskolowski / Katrin M Khakzar / Zeynel Ulusoy / Annalena Wallisch / Ahmad Jomaa / Gundula Hunaeus / Alain Scaiola / ...Authors: Martin Gamerdinger / Min Jia / Renate Schloemer / Laurenz Rabl / Mateusz Jaskolowski / Katrin M Khakzar / Zeynel Ulusoy / Annalena Wallisch / Ahmad Jomaa / Gundula Hunaeus / Alain Scaiola / Kay Diederichs / Nenad Ban / Elke Deuerling / Abstract: N-terminal methionine excision from newly synthesized proteins, catalyzed cotranslationally by methionine aminopeptidases (METAPs), is an essential and universally conserved process that plays a key ...N-terminal methionine excision from newly synthesized proteins, catalyzed cotranslationally by methionine aminopeptidases (METAPs), is an essential and universally conserved process that plays a key role in cell homeostasis and protein biogenesis. However, how METAPs interact with ribosomes and how their cleavage specificity is ensured is unknown. We discovered that in eukaryotes the nascent polypeptide-associated complex (NAC) controls ribosome binding of METAP1. NAC recruits METAP1 using a long, flexible tail and provides a platform for the formation of an active methionine excision complex at the ribosomal tunnel exit. This mode of interaction ensures the efficient excision of methionine from cytosolic proteins, whereas proteins targeted to the endoplasmic reticulum are spared. Our results suggest a broader mechanism for how access of protein biogenesis factors to translating ribosomes is controlled.
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