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Yorodumi- EMDB-50126: Mammalian quaternary complex of a translating 80S ribosome, NAC, ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50126 | ||||||||||||||||||
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Title | Mammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPK | ||||||||||||||||||
Map data | homogeneously refined cryo-EM map of the RNC-NAC-NatA/E-MetAP1-HYPK complex | ||||||||||||||||||
Sample |
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Keywords | translation / ribosome / NAC / N-terminal acetyltransferase / NatA / NatE / MetAP1 / HYPK | ||||||||||||||||||
Function / homology | Function and homology information negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / nascent polypeptide-associated complex / negative regulation of protein localization to endoplasmic reticulum / regulation of skeletal muscle fiber development / : / negative regulation of striated muscle cell apoptotic process / mitotic sister chromatid cohesion, centromeric / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / nascent polypeptide-associated complex / negative regulation of protein localization to endoplasmic reticulum / regulation of skeletal muscle fiber development / : / negative regulation of striated muscle cell apoptotic process / mitotic sister chromatid cohesion, centromeric / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / positive regulation of cell proliferation involved in heart morphogenesis / N-terminal protein amino acid acetylation / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / positive regulation of skeletal muscle tissue growth / cardiac ventricle development / peptide alpha-N-acetyltransferase activity / N-terminal protein amino acid modification / peptidyl-methionine modification / skeletal muscle tissue regeneration / N-acetyltransferase activity / histone H4 acetyltransferase activity / heart trabecula morphogenesis / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / ribosomal subunit / establishment of mitotic sister chromatid cohesion / negative regulation of formation of translation preinitiation complex / metalloexopeptidase activity / GAIT complex / regulation of G1 to G0 transition / exit from mitosis / laminin receptor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / mitotic sister chromatid cohesion / retinal ganglion cell axon guidance / mammalian oogenesis stage / homeostatic process / protein acetylation / G1 to G0 transition / internal protein amino acid acetylation / activation-induced cell death of T cells / macrophage chemotaxis / lung morphogenesis / metalloaminopeptidase activity / positive regulation of signal transduction by p53 class mediator / protein maturation / ubiquitin ligase inhibitor activity / phagocytic cup / 90S preribosome / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chromosome organization / T cell proliferation involved in immune response / protein-RNA complex assembly / erythrocyte development / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / aminopeptidase activity / ribosomal small subunit export from nucleus / translation regulator activity / laminin binding / rough endoplasmic reticulum / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / gastrulation / MDM2/MDM4 family protein binding / protein folding chaperone / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cytosolic ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / positive regulation of translation / small-subunit processome / protein kinase C binding / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / wound healing / placenta development / cellular response to gamma radiation / cellular response to type II interferon / platelet aggregation / mRNA 5'-UTR binding / transcription coactivator binding / spindle / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / G1/S transition of mitotic cell cycle / protein tag activity / rRNA processing Similarity search - Function | ||||||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Homo sapiens (human) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.26 Å | ||||||||||||||||||
Authors | Yudin D / Scaiola A / Ban N | ||||||||||||||||||
Funding support | United States, Germany, Switzerland, European Union, 5 items
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Citation | Journal: Nature / Year: 2024 Title: NAC guides a ribosomal multienzyme complex for nascent protein processing. Authors: Alfred M Lentzsch / Denis Yudin / Martin Gamerdinger / Sowmya Chandrasekar / Laurenz Rabl / Alain Scaiola / Elke Deuerling / Nenad Ban / Shu-Ou Shan / Abstract: Approximately 40% of the mammalian proteome undergoes N-terminal methionine excision and acetylation, mediated sequentially by methionine aminopeptidase (MetAP) and N-acetyltransferase A (NatA), ...Approximately 40% of the mammalian proteome undergoes N-terminal methionine excision and acetylation, mediated sequentially by methionine aminopeptidase (MetAP) and N-acetyltransferase A (NatA), respectively. Both modifications are strictly cotranslational and essential in higher eukaryotic organisms. The interaction, activity and regulation of these enzymes on translating ribosomes are poorly understood. Here we perform biochemical, structural and in vivo studies to demonstrate that the nascent polypeptide-associated complex (NAC) orchestrates the action of these enzymes. NAC assembles a multienzyme complex with MetAP1 and NatA early during translation and pre-positions the active sites of both enzymes for timely sequential processing of the nascent protein. NAC further releases the inhibitory interactions from the NatA regulatory protein huntingtin yeast two-hybrid protein K (HYPK) to activate NatA on the ribosome, enforcing cotranslational N-terminal acetylation. Our results provide a mechanistic model for the cotranslational processing of proteins in eukaryotic cells. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50126.map.gz | 337 MB | EMDB map data format | |
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Header (meta data) | emd-50126-v30.xml emd-50126.xml | 136.7 KB 136.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_50126_fsc.xml | 21 KB | Display | FSC data file |
Images | emd_50126.png | 165.7 KB | ||
Masks | emd_50126_msk_1.map emd_50126_msk_2.map | 669.9 MB 669.9 MB | Mask map | |
Filedesc metadata | emd-50126.cif.gz | 25.4 KB | ||
Others | emd_50126_additional_1.map.gz emd_50126_additional_2.map.gz emd_50126_half_map_1.map.gz emd_50126_half_map_2.map.gz | 34.1 MB 627.2 MB 622.4 MB 622.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50126 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50126 | HTTPS FTP |
-Validation report
Summary document | emd_50126_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_50126_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_50126_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | emd_50126_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50126 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50126 | HTTPS FTP |
-Related structure data
Related structure data | 9f1dMC 9f1bC 9f1cC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_50126.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | homogeneously refined cryo-EM map of the RNC-NAC-NatA/E-MetAP1-HYPK complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_50126_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_50126_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: main map lowpass filtered to estimated local resolution
File | emd_50126_additional_1.map | ||||||||||||
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Annotation | main map lowpass filtered to estimated local resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: main map lowpass filtered to 6 A resolution
File | emd_50126_additional_2.map | ||||||||||||
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Annotation | main map lowpass filtered to 6 A resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap A
File | emd_50126_half_map_1.map | ||||||||||||
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Annotation | halfmap A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap B
File | emd_50126_half_map_2.map | ||||||||||||
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Annotation | halfmap B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Quaternary complex of a translating 80S ribosome, NAC, MetAP1 and...
+Supramolecule #1: Quaternary complex of a translating 80S ribosome, NAC, MetAP1 and...
+Supramolecule #2: Rabbit ribosome-nascent chain complex
+Supramolecule #3: Human NAC heterodimer
+Supramolecule #4: Human methionine aminopeptidase 1
+Supramolecule #5: Human NatA/E-HYPK complex
+Supramolecule #6: Human NatA complex
+Supramolecule #7: Human HYPK
+Supramolecule #8: Human NatE with a GST tag
+Macromolecule #1: 28S rRNA
+Macromolecule #5: mRNA
+Macromolecule #7: 5S rRNA
+Macromolecule #8: P-site tRNA
+Macromolecule #10: 5.8S rRNA
+Macromolecule #68: 18S rRNA
+Macromolecule #2: 60S ribosomal protein L21
+Macromolecule #3: 60S ribosomal protein L29
+Macromolecule #4: 60S ribosomal protein L12
+Macromolecule #6: 40S ribosomal protein eS17
+Macromolecule #9: Small ribosomal subunit protein uS13
+Macromolecule #11: 60S ribosomal protein L22
+Macromolecule #12: 40S ribosomal protein S19
+Macromolecule #13: Large ribosomal subunit protein uL2
+Macromolecule #14: Ribosomal protein L23
+Macromolecule #15: 40S ribosomal protein uS10
+Macromolecule #16: Ribosomal protein L3
+Macromolecule #17: Large ribosomal subunit protein uL22
+Macromolecule #18: Ribosomal protein L26
+Macromolecule #19: Ribosomal protein S15a
+Macromolecule #20: Large ribosomal subunit protein uL18
+Macromolecule #21: Large ribosomal subunit protein uL23
+Macromolecule #22: Large ribosomal subunit protein eL18
+Macromolecule #23: 60S ribosomal protein L27
+Macromolecule #24: 40S ribosomal protein S23
+Macromolecule #25: 60S ribosomal protein L6
+Macromolecule #26: Ribosomal protein L24
+Macromolecule #27: Small ribosomal subunit protein eS21
+Macromolecule #28: 60S ribosomal protein L27a
+Macromolecule #29: 40S ribosomal protein S24
+Macromolecule #30: Ribosomal Protein uL30
+Macromolecule #31: Ribosomal protein L19
+Macromolecule #32: Small ribosomal subunit protein uS2
+Macromolecule #33: 40S ribosomal protein S25
+Macromolecule #34: Large ribosomal subunit protein eL8
+Macromolecule #35: Large ribosomal subunit protein uL4
+Macromolecule #36: Large ribosomal subunit protein eL20
+Macromolecule #37: 40S ribosomal protein S3a
+Macromolecule #38: 60S ribosomal protein L41
+Macromolecule #39: 60S ribosomal protein L9
+Macromolecule #40: Methionine aminopeptidase 1
+Macromolecule #41: Small ribosomal subunit protein uS5
+Macromolecule #42: 60S ribosomal protein L30
+Macromolecule #43: 60S ribosomal protein L10
+Macromolecule #44: Nascent polypeptide-associated complex subunit alpha
+Macromolecule #45: 40S ribosomal protein S3
+Macromolecule #46: 60S ribosomal protein L31
+Macromolecule #47: 60S ribosomal protein L11
+Macromolecule #48: Isoform 2 of Transcription factor BTF3
+Macromolecule #49: 40S ribosomal protein S4
+Macromolecule #50: Ribosomal protein L32
+Macromolecule #51: Nascent chain
+Macromolecule #52: Glutathione S-transferase class-mu 26 kDa isozyme,N-alpha-acetylt...
+Macromolecule #53: Ribosomal protein S5
+Macromolecule #54: 60S ribosomal protein L35a
+Macromolecule #55: Large ribosomal subunit protein eL13
+Macromolecule #56: N-alpha-acetyltransferase 15, NatA auxiliary subunit
+Macromolecule #57: 40S ribosomal protein S6
+Macromolecule #58: 60S ribosomal protein L34
+Macromolecule #59: 60S ribosomal protein L14
+Macromolecule #60: N-alpha-acetyltransferase 10
+Macromolecule #61: 40S ribosomal protein S7
+Macromolecule #62: 60S ribosomal protein L35
+Macromolecule #63: Ribosomal protein L15
+Macromolecule #64: Isoform 2 of Huntingtin-interacting protein K
+Macromolecule #65: 40S ribosomal protein S8
+Macromolecule #66: 60S ribosomal protein L36
+Macromolecule #67: Large ribosomal subunit protein uL13
+Macromolecule #69: 40S ribosomal protein S9
+Macromolecule #70: Ribosomal protein L37
+Macromolecule #71: 40S ribosomal protein S27
+Macromolecule #72: S10_plectin domain-containing protein
+Macromolecule #73: 60S ribosomal protein L38
+Macromolecule #74: 40S ribosomal protein S28
+Macromolecule #75: 40S ribosomal protein S11
+Macromolecule #76: 60S ribosomal protein L39-like
+Macromolecule #77: Ribosomal protein S27a
+Macromolecule #78: 40S ribosomal protein S12
+Macromolecule #79: Ubiquitin-ribosomal protein eL40 fusion protein
+Macromolecule #80: 40S ribosomal protein S30
+Macromolecule #81: 40S ribosomal protein S13
+Macromolecule #82: Large ribosomal subunit protein eL42
+Macromolecule #83: Small ribosomal subunit protein eS26
+Macromolecule #84: Small ribosomal subunit protein uS11
+Macromolecule #85: 60S ribosomal protein L37a
+Macromolecule #86: Small ribosomal subunit protein RACK1
+Macromolecule #87: 40S ribosomal protein uS19
+Macromolecule #88: Large ribosomal subunit protein eL28
+Macromolecule #89: 40S ribosomal protein S29
+Macromolecule #90: Small ribosomal subunit protein uS9
+Macromolecule #91: Large ribosomal subunit protein uL10
+Macromolecule #92: UNKNOWN ATOM OR ION
+Macromolecule #93: SPERMIDINE
+Macromolecule #94: MAGNESIUM ION
+Macromolecule #95: SPERMINE
+Macromolecule #96: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #97: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #98: ZINC ION
+Macromolecule #99: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |