[English] 日本語

- PDB-9qqb: Quaternary complex of a translating ribosome, NAC, NMT1, and NatA -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 9qqb | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Quaternary complex of a translating ribosome, NAC, NMT1, and NatA | ||||||||||||
![]() |
| ||||||||||||
![]() | RIBOSOME / Translation / co-translational protein processing | ||||||||||||
Function / homology | ![]() negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / negative regulation of striated muscle cell apoptotic process / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / regulation of skeletal muscle fiber development / protein-N-terminal-glutamate acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / positive regulation of cell proliferation involved in heart morphogenesis / N-terminal protein amino acid acetylation ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / negative regulation of striated muscle cell apoptotic process / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / regulation of skeletal muscle fiber development / protein-N-terminal-glutamate acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / positive regulation of cell proliferation involved in heart morphogenesis / N-terminal protein amino acid acetylation / myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / [histone H4]-lysine20 N-methyltransferase / NatA complex / positive regulation of skeletal muscle tissue growth / protein N-terminal-serine acetyltransferase activity / Late Phase of HIV Life Cycle / protein-N-terminal-alanine acetyltransferase activity / histone H4K20 methyltransferase activity / ketone metabolic process / regulation of opsin-mediated signaling pathway / cardiac ventricle development / protein-N-terminal amino-acid acetyltransferase activity / internal protein amino acid acetylation / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / N-acetyltransferase activity / heart trabecula morphogenesis / skeletal muscle tissue regeneration / acetyltransferase activator activity / S-adenosyl-L-methionine binding / protein localization to membrane / ribosomal subunit / laminin receptor activity / protein acetylation / positive regulation of double-strand break repair via nonhomologous end joining / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / positive regulation of signal transduction by p53 class mediator / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / chromosome organization / Major pathway of rRNA processing in the nucleolus and cytosol / phagocytic cup / pericentric heterochromatin / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / ribosomal small subunit export from nucleus / laminin binding / rough endoplasmic reticulum / eNOS activation / translation regulator activity / gastrulation / MDM2/MDM4 family protein binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / cellular response to interleukin-4 / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / 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 / small-subunit processome / wound healing / spindle / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / rhythmic process / positive regulation of canonical Wnt signaling pathway / Inactivation, recovery and regulation of the phototransduction cascade / protein transport / large ribosomal subunit / heparin binding / regulation of translation / ribosome binding / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å | ||||||||||||
![]() | Echeverria, B. / Jaskolowski, M. / Scaiola, A. / Ban, N. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() 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. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 6.6 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 454 KB | Display | |
Data in CIF | ![]() | 750.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 53296MC ![]() 9qqaC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
+RNA chain , 5 types, 5 molecules B5B7B8A2AT
+Large ribosomal subunit protein ... , 10 types, 10 molecules BABCBDBLBOBPBSBXBoBs
+Ribosomal protein ... , 10 types, 10 molecules BBBFBNBRBVBWBYBeBjBv
+60S ribosomal protein ... , 21 types, 21 molecules BEBGBHBIBJBMBTBUBZBaBbBcBdBfBgBhBiBkBlBpBt
+Protein/peptide , 1 types, 1 molecules BK
+Protein , 8 types, 8 molecules BQBrNtNuMAADAEAj
+Ubiquitin-ribosomal protein ... , 2 types, 2 molecules BmAC
+N-alpha-acetyltransferase ... , 2 types, 2 molecules XAXB
+Small ribosomal subunit protein ... , 20 types, 20 molecules AAABAFAGAZAeAiAkAlAmAnAoApAqArAtAuAvAyAz
+40S ribosomal protein ... , 10 types, 10 molecules AaAbAcAdAfAgAhAsAwAx
+Non-polymers , 7 types, 2696 molecules 












+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Quaternary complex of translating ribosome, NAC, NMT1 and NatA Type: RIBOSOME / Entity ID: #1-#13, #15-#89 / Source: NATURAL |
---|---|
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
EM software | Name: PHENIX / Version: 1.21.2_5419 / Category: model refinement |
---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15709 / Symmetry type: POINT |
Refinement | Cross valid method: NONE |