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Open data
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Basic information
| Entry | Database: PDB / ID: 9qlp | ||||||||||||||||||||||||||||||
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| Title | NMT1-NAC bound human RNC with full length ARF1 - State 2 | ||||||||||||||||||||||||||||||
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Keywords | RIBOSOME / co-translational / N-terminal myristoylation / myristoylation / NMT1 / ARF1 / NAC | ||||||||||||||||||||||||||||||
| Function / homology | Function and homology informationnegative regulation of striated muscle cell apoptotic process / myristoyltransferase activity / regulation of skeletal muscle fiber development / 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 / N-terminal protein myristoylation / positive regulation of skeletal muscle tissue growth / translation termination factor activity ...negative regulation of striated muscle cell apoptotic process / myristoyltransferase activity / regulation of skeletal muscle fiber development / 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 / N-terminal protein myristoylation / positive regulation of skeletal muscle tissue growth / translation termination factor activity / ketone metabolic process / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / regulation of opsin-mediated signaling pathway / Glycosphingolipid transport / positive regulation of protein localization to mitochondrion / translation release factor complex / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / cardiac ventricle development / regulation of receptor internalization / Activation, myristolyation of BID and translocation to mitochondria / Intra-Golgi traffic / cytoplasmic translational termination / regulation of Arp2/3 complex-mediated actin nucleation / heart trabecula morphogenesis / regulation of translational termination / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / translation release factor activity / Synthesis of PIPs at the Golgi membrane / translation release factor activity, codon specific / skeletal muscle tissue regeneration / Nef Mediated CD4 Down-regulation / protein methylation / translation at presynapse / optic nerve development / response to insecticide / alpha-beta T cell differentiation / exit from mitosis / sequence-specific mRNA binding / regulation of translation involved in cellular response to UV / dendritic spine organization / long-term synaptic depression / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / negative regulation of endoplasmic reticulum unfolded protein response / regulation of G1 to G0 transition / axial mesoderm development / retinal ganglion cell axon guidance / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / peptidyl-tRNA hydrolase activity / middle ear morphogenesis / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / 90S preribosome assembly / protein localization to membrane / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / positive regulation of ubiquitin-protein transferase activity / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / positive regulation of DNA-templated transcription initiation / nucleolus organization / TNFR1-mediated ceramide production / negative regulation of formation of translation preinitiation complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / PD-L1(CD274) glycosylation and translocation to plasma membrane / GAIT complex / negative regulation of RNA splicing / Enterobacterial factors antagonize host defense / COPI-dependent Golgi-to-ER retrograde traffic / TORC2 complex binding / G1 to G0 transition / supercoiled DNA binding / negative regulation of DNA repair / erythrocyte homeostasis / blastocyst development / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / Lysosome Vesicle Biogenesis / NF-kappaB complex / cytoplasmic translational initiation / rRNA modification in the nucleus and cytosol / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / negative regulation of phagocytosis / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / negative regulation of myoblast fusion / cytoplasmic side of rough endoplasmic reticulum membrane / Golgi Associated Vesicle Biogenesis / Formation of the ternary complex, and subsequently, the 43S complex / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / ion channel inhibitor activity Similarity search - Function | ||||||||||||||||||||||||||||||
| Biological species | Homo sapiens (human) | ||||||||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å | ||||||||||||||||||||||||||||||
Authors | Denk, T. / Berninghausen, O. / Beckmann, R. | ||||||||||||||||||||||||||||||
| Funding support | Germany, 1items
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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. | ||||||||||||||||||||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9qlp.cif.gz | 5.5 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb9qlp.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 9qlp.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/9qlp ftp://data.pdbj.org/pub/pdb/validation_reports/ql/9qlp | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 53231MC ![]() 9i2dC ![]() 9i2eC ![]() 9qloC ![]() 9qlqC ![]() 9s3bC ![]() 9s3cC ![]() 9s3dC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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Components
-RNA chain , 6 types, 6 molecules CMCPL5L7L8S2
| #1: RNA chain | Mass: 306714.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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| #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: 602777.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 151415227 |
-Protein , 12 types, 12 molecules CRCZLILmLsNANBNMSESeSfSg
| #3: Protein | Mass: 49107.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Naturally occurring K63 hydroxylation / Source: (natural) Homo sapiens (human) / References: UniProt: P62495 |
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| #4: Protein | Mass: 24539.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARF1 / Production host: Homo sapiens (human) / References: UniProt: P84077, small monomeric GTPase |
| #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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13765 |
| #53: Protein | Mass: 17724.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P20290 |
| #54: Protein | Mass: 56884.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
| #60: Protein | Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701 |
| #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 ... , 37 types, 37 molecules LALBLCLDLGLHLJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLeLfLgLh...
-Large ribosomal subunit protein ... , 4 types, 4 molecules LELFLjLt
| #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 |
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| #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 |
| #42: Protein | Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927 |
| #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 ... , 29 types, 29 molecules SASBSCSDSFSGSHSISJSKSLSMSNSOSPSQSRSSSTSUSVSWSXSYSZSaSbScSd
-Non-polymers , 4 types, 211 molecules 






| #89: Chemical | ChemComp-MG / #90: Chemical | ChemComp-G3D / | #91: Chemical | ChemComp-ZN / #92: Water | ChemComp-HOH / | |
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-Details
| Has ligand of interest | N |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
| Component | Name: NMT1-NAC bound human RNC with full length ARF1 - State 2 Type: RIBOSOME Entity ID: #1-#3, #5-#47, #49-#51, #55-#88, #52-#53, #4, #54 Source: NATURAL |
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| 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 |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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| 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) |
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Processing
| EM software | Name: PHENIX / Version: 1.21.2_5419: / Category: model refinement |
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
| 3D reconstruction | Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21642 / Symmetry type: POINT |
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About Yorodumi




Homo sapiens (human)
Germany, 1items
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FIELD EMISSION GUN