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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | NAC bound human RNC with 58 amino acid ARF1-linker | |||||||||
Map data | NAC bound human RNC with 58 amino acid ARF1-linker - homogeneous refinement - local resolution filtered | |||||||||
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Keywords | co-translational / N-terminal myristoylation / myristoylation / NAC / ARF1 / NMT1 / RIBOSOME | |||||||||
| Function / homology | Function and homology informationnegative regulation of striated muscle cell apoptotic process / regulation of skeletal muscle fiber development / positive regulation of cell proliferation involved in heart morphogenesis / positive regulation of skeletal muscle tissue growth / translation termination factor activity / translation release factor complex / cardiac ventricle development / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / cytoplasmic translational termination ...negative regulation of striated muscle cell apoptotic process / regulation of skeletal muscle fiber development / positive regulation of cell proliferation involved in heart morphogenesis / positive regulation of skeletal muscle tissue growth / translation termination factor activity / translation release factor complex / cardiac ventricle development / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / cytoplasmic translational termination / heart trabecula morphogenesis / regulation of translational termination / translation release factor activity / skeletal muscle tissue regeneration / translation release factor activity, codon specific / male meiosis I / translation at presynapse / response to insecticide / sequence-specific mRNA binding / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / negative regulation of endoplasmic reticulum unfolded protein response / regulation of G1 to G0 transition / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / peptidyl-tRNA hydrolase activity / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein methylation / protein tyrosine kinase inhibitor activity / G1 to G0 transition / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of formation of translation preinitiation complex / positive regulation of ubiquitin-protein transferase activity / GAIT complex / nucleolus organization / positive regulation of DNA-templated transcription initiation / negative regulation of RNA splicing / negative regulation of DNA repair / TORC2 complex binding / positive regulation of DNA damage response, signal transduction by p53 class mediator / erythrocyte homeostasis / supercoiled DNA binding / regulation of establishment of cell polarity / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / 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 / negative regulation of phagocytosis / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / negative regulation of myoblast fusion / ion channel inhibitor activity / positive regulation of mitochondrial depolarization / protein kinase A binding / Ribosomal scanning and start codon recognition / Translation initiation complex formation / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / Protein hydroxylation / TOR signaling / negative regulation of translational frameshifting / BH3 domain binding / iron-sulfur cluster binding / monocyte chemotaxis / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / mTORC1-mediated signalling / gastrulation / SARS-CoV-1 modulates host translation machinery / regulation of cell division / protein localization to nucleus / positive regulation of GTPase activity / Peptide chain elongation / cellular response to ethanol / protein targeting / Selenocysteine synthesis / Formation of a pool of free 40S subunits / negative regulation of protein binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein serine/threonine kinase inhibitor activity / negative regulation of respiratory burst involved in inflammatory response / Eukaryotic Translation Termination / Dengue Virus Attachment and Entry / negative regulation of ubiquitin-dependent protein catabolic process / ubiquitin ligase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.32 Å | |||||||||
Authors | Denk T / Berninghausen O / Beckmann R | |||||||||
| Funding support | Germany, 1 items
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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. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_54530.map.gz | 143 MB | EMDB map data format | |
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| Header (meta data) | emd-54530-v30.xml emd-54530.xml | 114.7 KB 114.7 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_54530_fsc.xml | 21.2 KB | Display | FSC data file |
| Images | emd_54530.png | 74.7 KB | ||
| Filedesc metadata | emd-54530.cif.gz | 21.8 KB | ||
| Others | emd_54530_additional_1.map.gz emd_54530_additional_2.map.gz emd_54530_half_map_1.map.gz emd_54530_half_map_2.map.gz | 502.4 MB 945.3 MB 928 MB 928 MB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-54530 ftp://data.pdbj.org/pub/emdb/structures/EMD-54530 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9s3dMC ![]() 9i2dC ![]() 9i2eC ![]() 9qloC ![]() 9qlpC ![]() 9qlqC ![]() 9s3bC ![]() 9s3cC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_54530.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | NAC bound human RNC with 58 amino acid ARF1-linker - homogeneous refinement - local resolution filtered | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.727 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: NAC bound human RNC with 58 amino acid...
| File | emd_54530_additional_1.map | ||||||||||||
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| Annotation | NAC bound human RNC with 58 amino acid ARF1-linker - homogeneous refinement | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Additional map: NAC bound human RNC with 58 amino acid...
| File | emd_54530_additional_2.map | ||||||||||||
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| Annotation | NAC bound human RNC with 58 amino acid ARF1-linker - homogeneous refinement - sharpened | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: NAC bound human RNC with 58 amino acid...
| File | emd_54530_half_map_1.map | ||||||||||||
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| Annotation | NAC bound human RNC with 58 amino acid ARF1-linker - homogeneous refinement - half map A | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: NAC bound human RNC with 58 amino acid...
| File | emd_54530_half_map_2.map | ||||||||||||
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| Annotation | NAC bound human RNC with 58 amino acid ARF1-linker - homogeneous refinement - half map B | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : NAC bound human RNC with 58 amino acid ARF1-linker
+Supramolecule #1: NAC bound human RNC with 58 amino acid ARF1-linker
+Macromolecule #1: Nascent polypeptide-associated complex subunit alpha
+Macromolecule #2: Isoform 2 of Transcription factor BTF3
+Macromolecule #5: Eukaryotic peptide chain release factor subunit 1
+Macromolecule #6: nascent chain
+Macromolecule #10: 60S ribosomal protein L8
+Macromolecule #11: 60S ribosomal protein L3
+Macromolecule #12: 60S ribosomal protein L4
+Macromolecule #13: 60S ribosomal protein L5
+Macromolecule #14: Large ribosomal subunit protein eL6
+Macromolecule #15: Large ribosomal subunit protein uL30
+Macromolecule #16: 60S ribosomal protein L7a
+Macromolecule #17: 60S ribosomal protein L9
+Macromolecule #18: Ribosomal protein uL16-like
+Macromolecule #19: 60S ribosomal protein L11
+Macromolecule #20: 60S ribosomal protein L13
+Macromolecule #21: 60S ribosomal protein L14
+Macromolecule #22: 60S ribosomal protein L15
+Macromolecule #23: 60S ribosomal protein L13a
+Macromolecule #24: 60S ribosomal protein L17
+Macromolecule #25: 60S ribosomal protein L18
+Macromolecule #26: 60S ribosomal protein L19
+Macromolecule #27: 60S ribosomal protein L18a
+Macromolecule #28: 60S ribosomal protein L21
+Macromolecule #29: 60S ribosomal protein L22
+Macromolecule #30: 60S ribosomal protein L23
+Macromolecule #31: 60S ribosomal protein L24
+Macromolecule #32: 60S ribosomal protein L23a
+Macromolecule #33: 60S ribosomal protein L26
+Macromolecule #34: 60S ribosomal protein L27
+Macromolecule #35: 60S ribosomal protein L27a
+Macromolecule #36: 60S ribosomal protein L29
+Macromolecule #37: 60S ribosomal protein L30
+Macromolecule #38: 60S ribosomal protein L31
+Macromolecule #39: 60S ribosomal protein L32
+Macromolecule #40: 60S ribosomal protein L35a
+Macromolecule #41: 60S ribosomal protein L34
+Macromolecule #42: 60S ribosomal protein L35
+Macromolecule #43: 60S ribosomal protein L36
+Macromolecule #44: Large ribosomal subunit protein eL37
+Macromolecule #45: 60S ribosomal protein L38
+Macromolecule #46: 60S ribosomal protein L39
+Macromolecule #47: Ubiquitin-60S ribosomal protein L40
+Macromolecule #48: 60S ribosomal protein L41
+Macromolecule #49: 60S ribosomal protein L36a
+Macromolecule #50: 60S ribosomal protein L37a
+Macromolecule #51: 60S ribosomal protein L28
+Macromolecule #52: 60S acidic ribosomal protein P0
+Macromolecule #53: Large ribosomal subunit protein uL11
+Macromolecule #55: 40S ribosomal protein SA
+Macromolecule #56: 40S ribosomal protein S3a
+Macromolecule #57: 40S ribosomal protein S2
+Macromolecule #58: 40S ribosomal protein S3
+Macromolecule #59: Small ribosomal subunit protein eS4, X isoform
+Macromolecule #60: 40S ribosomal protein S5
+Macromolecule #61: 40S ribosomal protein S6
+Macromolecule #62: 40S ribosomal protein S7
+Macromolecule #63: 40S ribosomal protein S8
+Macromolecule #64: 40S ribosomal protein S9
+Macromolecule #65: 40S ribosomal protein S10
+Macromolecule #66: 40S ribosomal protein S11
+Macromolecule #67: 40S ribosomal protein S12
+Macromolecule #68: 40S ribosomal protein S13
+Macromolecule #69: 40S ribosomal protein S14
+Macromolecule #70: 40S ribosomal protein S15
+Macromolecule #71: 40S ribosomal protein S16
+Macromolecule #72: 40S ribosomal protein S17
+Macromolecule #73: 40S ribosomal protein S18
+Macromolecule #74: 40S ribosomal protein S19
+Macromolecule #75: 40S ribosomal protein S20
+Macromolecule #76: 40S ribosomal protein S21
+Macromolecule #77: 40S ribosomal protein S15a
+Macromolecule #78: 40S ribosomal protein S23
+Macromolecule #79: 40S ribosomal protein S24
+Macromolecule #80: 40S ribosomal protein S25
+Macromolecule #81: 40S ribosomal protein S26
+Macromolecule #82: 40S ribosomal protein S27
+Macromolecule #83: 40S ribosomal protein S28
+Macromolecule #84: 40S ribosomal protein S29
+Macromolecule #85: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
+Macromolecule #86: Ubiquitin
+Macromolecule #87: Receptor of activated protein C kinase 1
+Macromolecule #3: 58 amino acid ARF1-linker - V5 peptide - hCMV staller mRNA
+Macromolecule #4: prolyl-tRNA
+Macromolecule #7: 28S rRNA
+Macromolecule #8: 5S rRNA
+Macromolecule #9: 5.8S rRNA
+Macromolecule #54: 18S rRNA
+Macromolecule #88: MAGNESIUM ION
+Macromolecule #89: ZINC ION
+Macromolecule #90: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi




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

