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Yorodumi- EMDB-54529: NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2 -
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Open data
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Basic information
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| Title | NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2 | |||||||||
Map data | NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2 - 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 / 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 | single particle reconstruction / cryo EM / Resolution: 2.42 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. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Adams PD | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_54529.map.gz | 142.9 MB | EMDB map data format | |
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| Header (meta data) | emd-54529-v30.xml emd-54529.xml | 117.3 KB 117.3 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_54529_fsc.xml | 21.2 KB | Display | FSC data file |
| Images | emd_54529.png | 78.6 KB | ||
| Filedesc metadata | emd-54529.cif.gz | 22.5 KB | ||
| Others | emd_54529_additional_1.map.gz emd_54529_additional_2.map.gz emd_54529_half_map_1.map.gz emd_54529_half_map_2.map.gz | 501.9 MB 946.1 MB 926.7 MB 926.7 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-54529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-54529 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9s3cMC ![]() 9i2dC ![]() 9i2eC ![]() 9qloC ![]() 9qlpC ![]() 9qlqC ![]() 9s3bC ![]() 9s3dC 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_54529.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2 - 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: NMT1-NAC bound human RNC with 58 amino acid...
| File | emd_54529_additional_1.map | ||||||||||||
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| Annotation | NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2 - homogeneous refinement | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Additional map: NMT1-NAC bound human RNC with 58 amino acid...
| File | emd_54529_additional_2.map | ||||||||||||
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| Annotation | NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2 - homogeneous refinement - sharpened | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: NMT1-NAC bound human RNC with 58 amino acid...
| File | emd_54529_half_map_1.map | ||||||||||||
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| Annotation | NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2 - homogeneous refinement - half map A | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: NMT1-NAC bound human RNC with 58 amino acid...
| File | emd_54529_half_map_2.map | ||||||||||||
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| Annotation | NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2 - homogeneous refinement - half map B | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2
+Supramolecule #1: NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2
+Macromolecule #1: 58 amino acid ARF1-linker - V5 peptide - hCMV staller mRNA
+Macromolecule #2: prolyl-tRNA
+Macromolecule #5: 28S rRNA
+Macromolecule #6: 5S rRNA
+Macromolecule #7: 5.8S rRNA
+Macromolecule #55: 18S rRNA
+Macromolecule #3: Eukaryotic peptide chain release factor subunit 1
+Macromolecule #4: nascent chain
+Macromolecule #8: 60S ribosomal protein L8
+Macromolecule #9: 60S ribosomal protein L3
+Macromolecule #10: 60S ribosomal protein L4
+Macromolecule #11: 60S ribosomal protein L5
+Macromolecule #12: Large ribosomal subunit protein eL6
+Macromolecule #13: Large ribosomal subunit protein uL30
+Macromolecule #14: 60S ribosomal protein L7a
+Macromolecule #15: 60S ribosomal protein L9
+Macromolecule #16: Ribosomal protein uL16-like
+Macromolecule #17: 60S ribosomal protein L11
+Macromolecule #18: 60S ribosomal protein L13
+Macromolecule #19: 60S ribosomal protein L14
+Macromolecule #20: 60S ribosomal protein L15
+Macromolecule #21: 60S ribosomal protein L13a
+Macromolecule #22: 60S ribosomal protein L17
+Macromolecule #23: 60S ribosomal protein L18
+Macromolecule #24: 60S ribosomal protein L19
+Macromolecule #25: 60S ribosomal protein L18a
+Macromolecule #26: 60S ribosomal protein L21
+Macromolecule #27: 60S ribosomal protein L22
+Macromolecule #28: 60S ribosomal protein L23
+Macromolecule #29: 60S ribosomal protein L24
+Macromolecule #30: 60S ribosomal protein L23a
+Macromolecule #31: 60S ribosomal protein L26
+Macromolecule #32: 60S ribosomal protein L27
+Macromolecule #33: 60S ribosomal protein L27a
+Macromolecule #34: 60S ribosomal protein L29
+Macromolecule #35: 60S ribosomal protein L30
+Macromolecule #36: 60S ribosomal protein L31
+Macromolecule #37: 60S ribosomal protein L32
+Macromolecule #38: 60S ribosomal protein L35a
+Macromolecule #39: 60S ribosomal protein L34
+Macromolecule #40: 60S ribosomal protein L35
+Macromolecule #41: 60S ribosomal protein L36
+Macromolecule #42: Large ribosomal subunit protein eL37
+Macromolecule #43: 60S ribosomal protein L38
+Macromolecule #44: 60S ribosomal protein L39
+Macromolecule #45: Ubiquitin-60S ribosomal protein L40
+Macromolecule #46: 60S ribosomal protein L41
+Macromolecule #47: 60S ribosomal protein L36a
+Macromolecule #48: 60S ribosomal protein L37a
+Macromolecule #49: 60S ribosomal protein L28
+Macromolecule #50: 60S acidic ribosomal protein P0
+Macromolecule #51: Large ribosomal subunit protein uL11
+Macromolecule #52: Nascent polypeptide-associated complex subunit alpha
+Macromolecule #53: Isoform 2 of Transcription factor BTF3
+Macromolecule #54: Glycylpeptide N-tetradecanoyltransferase 1
+Macromolecule #56: 40S ribosomal protein SA
+Macromolecule #57: 40S ribosomal protein S3a
+Macromolecule #58: 40S ribosomal protein S2
+Macromolecule #59: 40S ribosomal protein S3
+Macromolecule #60: Small ribosomal subunit protein eS4, X isoform
+Macromolecule #61: 40S ribosomal protein S5
+Macromolecule #62: 40S ribosomal protein S6
+Macromolecule #63: 40S ribosomal protein S7
+Macromolecule #64: 40S ribosomal protein S8
+Macromolecule #65: 40S ribosomal protein S9
+Macromolecule #66: 40S ribosomal protein S10
+Macromolecule #67: 40S ribosomal protein S11
+Macromolecule #68: 40S ribosomal protein S12
+Macromolecule #69: 40S ribosomal protein S13
+Macromolecule #70: 40S ribosomal protein S14
+Macromolecule #71: 40S ribosomal protein S15
+Macromolecule #72: 40S ribosomal protein S16
+Macromolecule #73: 40S ribosomal protein S17
+Macromolecule #74: 40S ribosomal protein S18
+Macromolecule #75: 40S ribosomal protein S19
+Macromolecule #76: 40S ribosomal protein S20
+Macromolecule #77: 40S ribosomal protein S21
+Macromolecule #78: 40S ribosomal protein S15a
+Macromolecule #79: 40S ribosomal protein S23
+Macromolecule #80: 40S ribosomal protein S24
+Macromolecule #81: 40S ribosomal protein S25
+Macromolecule #82: 40S ribosomal protein S26
+Macromolecule #83: 40S ribosomal protein S27
+Macromolecule #84: 40S ribosomal protein S28
+Macromolecule #85: 40S ribosomal protein S29
+Macromolecule #86: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
+Macromolecule #87: Ubiquitin
+Macromolecule #88: Receptor of activated protein C kinase 1
+Macromolecule #89: MAGNESIUM ION
+Macromolecule #90: ZINC ION
+Macromolecule #91: 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

