+
Open data
-
Basic information
| Entry | Database: PDB / ID: 9i2d | ||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Title | NMT1-NAC bound human RNC with 10 amino acid ARF1-linker | ||||||||||||||||||||||||||||||
Components |
| ||||||||||||||||||||||||||||||
Keywords | RIBOSOME / myristoylation / NMT1 / co-translational / NAC / RNC | ||||||||||||||||||||||||||||||
| Function / homology | Function and homology informationnegative regulation of striated muscle cell apoptotic process / regulation of skeletal muscle fiber development / myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / positive regulation of cell proliferation involved in heart morphogenesis / Late Phase of HIV Life Cycle / positive regulation of skeletal muscle tissue growth / translation termination factor activity / ketone metabolic process ...negative regulation of striated muscle cell apoptotic process / regulation of skeletal muscle fiber development / myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / positive regulation of cell proliferation involved in heart morphogenesis / Late Phase of HIV Life Cycle / positive regulation of skeletal muscle tissue growth / translation termination factor activity / ketone metabolic process / regulation of opsin-mediated signaling pathway / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / translation release factor complex / cardiac ventricle development / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of protein localization to mitochondrion / cytoplasmic translational termination / regulation of translational termination / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / translation release factor activity / translation release factor activity, codon specific / heart trabecula morphogenesis / skeletal muscle tissue regeneration / protein methylation / translation at presynapse / exit from mitosis / optic nerve development / response to insecticide / eukaryotic 80S initiation complex / sequence-specific mRNA binding / regulation of translation involved in cellular response to UV / negative regulation of formation of translation preinitiation complex / axial mesoderm development / regulation of G1 to G0 transition / retinal ganglion cell axon guidance / negative regulation of endoplasmic reticulum unfolded protein response / ribosomal protein import into nucleus / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of respiratory burst involved in inflammatory response / positive regulation of ubiquitin-protein transferase activity / positive regulation of gastrulation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / IRE1-RACK1-PP2A complex / protein localization to membrane / positive regulation of Golgi to plasma membrane protein transport / peptidyl-tRNA hydrolase activity / alpha-beta T cell differentiation / nucleolus organization / positive regulation of DNA-templated transcription initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / TNFR1-mediated ceramide production / GAIT complex / negative regulation of RNA splicing / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / supercoiled DNA binding / neural crest cell differentiation / NF-kappaB complex / negative regulation of DNA repair / G1 to G0 transition / oxidized purine DNA binding / cytoplasmic translational initiation / cysteine-type endopeptidase activator activity involved in apoptotic process / middle ear morphogenesis / regulation of establishment of cell polarity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / rRNA modification in the nucleus and cytosol / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / protein kinase A binding / ion channel inhibitor activity / Ribosomal scanning and start codon recognition / laminin receptor activity / homeostatic process / pigmentation / Translation initiation complex formation / positive regulation of mitochondrial depolarization / macrophage chemotaxis / lung morphogenesis / negative regulation of Wnt signaling pathway / positive regulation of natural killer cell proliferation / fibroblast growth factor binding / male meiosis I / monocyte chemotaxis / BH3 domain binding / negative regulation of translational frameshifting / TOR signaling / Protein hydroxylation Similarity search - Function | ||||||||||||||||||||||||||||||
| Biological species | Homo sapiens (human) | ||||||||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.19 Å | ||||||||||||||||||||||||||||||
Authors | Denk, T. / Berninghausen, O. / Beckmann, R. | ||||||||||||||||||||||||||||||
| Funding support | Germany, 1items
| ||||||||||||||||||||||||||||||
Citation | Journal: Nat Commun / Year: 2026Title: Structural basis of co-translational N-myristoylation in humans. Authors: Timo Denk / Paul Monassa / Joanna Musial / Otto Berninghausen / Birgitta Beatrix / Carmela Giglione / Thierry Meinnel / Roland Beckmann / ![]() Abstract: Modifications of proteins occurring during translation are critical for protein localization, stability and function. N-myristoylation is an essential N-terminal lipid modification catalyzed co- ...Modifications of proteins occurring during translation are critical for protein localization, stability and function. N-myristoylation is an essential N-terminal lipid modification catalyzed co-translationally by N-myristoyltransferases (NMTs) which have been identified as promising drug targets. However, its molecular basis in the context of the translating ribosome is not known. Here, we reveal the structural basis for co-translational N-myristoylation by NMT1 on the human ribosome by cryo-electron microscopy (cryo-EM). We show that NMT1 binds near the peptide tunnel exit and interacts with the nascent polypeptide-associated complex (NAC). Unlike other multi-enzyme complexes that act simultaneously, we find that methionine excision by methionine aminopeptidases and N-myristoylation occur sequentially via consecutive binding to the ribosome. Furthermore, our data suggest that NMT1 remains associated with elongating nascent chains, indicating a co-translational chaperone-like function in partnership with NAC. These insights provide a molecular foundation for the understanding of the co-translational N-myristoylation mechanism in humans. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / ![]() Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | ||||||||||||||||||||||||||||||
| History |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 9i2d.cif.gz | 6.7 MB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb9i2d.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 9i2d.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/9i2d ftp://data.pdbj.org/pub/pdb/validation_reports/i2/9i2d | HTTPS FTP |
|---|
-Related structure data
| Related structure data | ![]() 52581MC ![]() 9i2eC ![]() 9qloC ![]() 9qlpC ![]() 9qlqC ![]() 9s3bC ![]() 9s3cC ![]() 9s3dC M: map data used to model this data C: citing same article ( |
|---|---|
| Similar structure data | Similarity search - Function & homology F&H Search |
-
Links
-
Assembly
| Deposited unit | ![]()
|
|---|---|
| 1 |
|
-
Components
-RNA chain , 6 types, 6 molecules CMCPL5L7L8S2
| #1: RNA chain | Mass: 131455.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
|---|---|
| #2: RNA chain | Mass: 24189.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
| #5: RNA chain | Mass: 1640222.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: NR_003287 |
| #6: RNA chain | Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898 |
| #7: RNA chain | Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853 |
| #55: RNA chain | Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 151415227 |
-Protein , 11 types, 11 molecules CRCZLILmLsNANBNMSeSfSg
| #3: Protein | Mass: 49107.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Hydroxylation of lysine 63 (LYO) is a naturally occurring protein modification of human eukaryotic release factor 1 (eRF1) Source: (natural) Homo sapiens (human) / References: UniProt: P62495 |
|---|---|
| #4: Protein | Mass: 6023.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
| #16: Protein | Mass: 24570.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96L21 |
| #45: Protein | Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987 |
| #50: Protein | Mass: 34309.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05388 |
| #52: Protein | Mass: 23406.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NACA, HSD48 / Production host: ![]() |
| #53: Protein | Mass: 17724.037 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BTF3, NACB, OK/SW-cl.8 / Production host: ![]() |
| #54: Protein | Mass: 56884.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1, NMT / Production host: ![]() References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
| #86: Protein | Mass: 14415.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861 |
| #87: Protein | Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979 |
| #88: Protein | Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244 |
+60S ribosomal protein ... , 38 types, 38 molecules LALBLCLDLGLHLJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLeLfLgLh...
-Large ribosomal subunit protein ... , 3 types, 3 molecules LELFLt
| #12: Protein | Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878 |
|---|---|
| #13: Protein | Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124 |
| #51: Protein | Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30050 |
+40S ribosomal protein ... , 30 types, 30 molecules SASBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSSSTSUSVSWSXSYSZSaSbScSd
-Non-polymers , 3 types, 210 molecules 




| #89: Chemical | ChemComp-MG / #90: Chemical | ChemComp-ZN / #91: Water | ChemComp-HOH / | |
|---|
-Details
| Has ligand of interest | N |
|---|---|
| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
|---|---|
| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
| Component | Name: NMT1-NAC bound human RNC with 10 amino acid ARF1-linker Type: RIBOSOME / Entity ID: #1-#88 / Source: NATURAL |
|---|---|
| Source (natural) | Organism: Homo sapiens (human) |
| Buffer solution | pH: 7.5 |
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
|---|---|
| Microscopy | Model: TFS KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm |
| Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k 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: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163265 / Symmetry type: POINT | ||||||||||||||||||||||||
| Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
| Displacement parameters | Biso mean: 41.7 Å2 | ||||||||||||||||||||||||
| Refine LS restraints |
|
Movie
Controller
About Yorodumi




Homo sapiens (human)
Germany, 1items
Citation















PDBj



























































FIELD EMISSION GUN