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Open data
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Basic information
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| Title | Yeast 80S ribosome in complex with Map1 (conformation 1) | |||||||||
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Keywords | translation / aminopeptidase / nascent chain / co-translational modification / Map1 / RIBOSOME | |||||||||
| Function / homology | Function and homology informationInactivation, recovery and regulation of the phototransduction cascade / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity ...Inactivation, recovery and regulation of the phototransduction cascade / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / metalloaminopeptidase activity / negative regulation of translational frameshifting / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / positive regulation of protein kinase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / regulation of translational fidelity / protein-RNA complex assembly / ribosomal subunit export from nucleus / maturation of LSU-rRNA / 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) / translation regulator activity / cytosolic ribosome / rescue of stalled ribosome / protein kinase C binding / cellular response to amino acid starvation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / macroautophagy / small-subunit processome / translational initiation / maintenance of translational fidelity / protein processing / modification-dependent protein catabolic process / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / ribonucleoprotein complex / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Knorr AG / Mackens-Kiani T / Musial J / Berninghausen O / Becker T / Beatrix B / Beckmann R | |||||||||
| Funding support | Germany, 1 items
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Citation | Journal: PLoS Biol / Year: 2023Title: The dynamic architecture of Map1- and NatB-ribosome complexes coordinates the sequential modifications of nascent polypeptide chains. Authors: Alexandra G Knorr / Timur Mackens-Kiani / Joanna Musial / Otto Berninghausen / Thomas Becker / Birgitta Beatrix / Roland Beckmann / ![]() Abstract: Cotranslational modification of the nascent polypeptide chain is one of the first events during the birth of a new protein. In eukaryotes, methionine aminopeptidases (MetAPs) cleave off the starter ...Cotranslational modification of the nascent polypeptide chain is one of the first events during the birth of a new protein. In eukaryotes, methionine aminopeptidases (MetAPs) cleave off the starter methionine, whereas N-acetyl-transferases (NATs) catalyze N-terminal acetylation. MetAPs and NATs compete with other cotranslationally acting chaperones, such as ribosome-associated complex (RAC), protein targeting and translocation factors (SRP and Sec61) for binding sites at the ribosomal tunnel exit. Yet, whereas well-resolved structures for ribosome-bound RAC, SRP and Sec61, are available, structural information on the mode of ribosome interaction of eukaryotic MetAPs or of the five cotranslationally active NATs is only available for NatA. Here, we present cryo-EM structures of yeast Map1 and NatB bound to ribosome-nascent chain complexes. Map1 is mainly associated with the dynamic rRNA expansion segment ES27a, thereby kept at an ideal position below the tunnel exit to act on the emerging substrate nascent chain. For NatB, we observe two copies of the NatB complex. NatB-1 binds directly below the tunnel exit, again involving ES27a, and NatB-2 is located below the second universal adapter site (eL31 and uL22). The binding mode of the two NatB complexes on the ribosome differs but overlaps with that of NatA and Map1, implying that NatB binds exclusively to the tunnel exit. We further observe that ES27a adopts distinct conformations when bound to NatA, NatB, or Map1, together suggesting a contribution to the coordination of a sequential activity of these factors on the emerging nascent chain at the ribosomal exit tunnel. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_16182.map.gz | 244.4 MB | EMDB map data format | |
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| Header (meta data) | emd-16182-v30.xml emd-16182.xml | 97 KB 97 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_16182_fsc.xml | 14.9 KB | Display | FSC data file |
| Images | emd_16182.png | 127.1 KB | ||
| Filedesc metadata | emd-16182.cif.gz | 18.4 KB | ||
| Others | emd_16182_half_map_1.map.gz emd_16182_half_map_2.map.gz | 225.4 MB 226.3 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16182 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16182 | HTTPS FTP |
-Validation report
| Summary document | emd_16182_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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| Full document | emd_16182_full_validation.pdf.gz | 1.2 MB | Display | |
| Data in XML | emd_16182_validation.xml.gz | 23.3 KB | Display | |
| Data in CIF | emd_16182_validation.cif.gz | 29.9 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16182 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16182 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8bqdMC ![]() 8bipC ![]() 8bjqC ![]() 8bqxC 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_16182.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #2
| File | emd_16182_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_16182_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : Yeast 80S ribosome in complex with Map1
+Supramolecule #1: Yeast 80S ribosome in complex with Map1
+Macromolecule #1: Rps5p
+Macromolecule #2: RPS3 isoform 1
+Macromolecule #3: 40S ribosomal protein S10-A
+Macromolecule #4: 40S ribosomal protein S12
+Macromolecule #5: 40S ribosomal protein S15
+Macromolecule #6: 40S ribosomal protein S16-A
+Macromolecule #7: 40S ribosomal protein S17-A
+Macromolecule #8: 40S ribosomal protein S18-A
+Macromolecule #9: 40S ribosomal protein S19-A
+Macromolecule #10: RPS20 isoform 1
+Macromolecule #11: 40S ribosomal protein S25
+Macromolecule #12: RPS28A isoform 1
+Macromolecule #13: RPS29A isoform 1
+Macromolecule #14: 40S ribosomal protein S31
+Macromolecule #15: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #16: 40S ribosomal protein S0-A
+Macromolecule #17: 40S ribosomal protein S1-A
+Macromolecule #18: RPS2 isoform 1
+Macromolecule #19: 40S ribosomal protein S4-A
+Macromolecule #20: 40S ribosomal protein S6-A
+Macromolecule #21: 40S ribosomal protein S7-A
+Macromolecule #22: 40S ribosomal protein S8-B
+Macromolecule #23: 40S ribosomal protein S9-A
+Macromolecule #24: 40S ribosomal protein S11-A
+Macromolecule #25: 40S ribosomal protein S13
+Macromolecule #26: 40S ribosomal protein S14-B
+Macromolecule #27: 60S ribosomal protein L8-A
+Macromolecule #28: 60S ribosomal protein L3
+Macromolecule #29: 60S ribosomal protein L23-A
+Macromolecule #30: 60S ribosomal protein L18-A
+Macromolecule #31: 60S ribosomal protein L36-A
+Macromolecule #32: 60S ribosomal protein L31-A
+Macromolecule #34: 40S ribosomal protein S21-A
+Macromolecule #35: RPS22A isoform 1
+Macromolecule #36: 40S ribosomal protein S23-A
+Macromolecule #37: 40S ribosomal protein S24-A
+Macromolecule #38: RPS26B isoform 1
+Macromolecule #39: 40S ribosomal protein S27-A
+Macromolecule #40: 40S ribosomal protein S30-A
+Macromolecule #44: 60S ribosomal protein L2-A
+Macromolecule #45: RPL4A isoform 1
+Macromolecule #46: RPL5 isoform 1
+Macromolecule #47: 60S ribosomal protein L6-B
+Macromolecule #48: 60S ribosomal protein L7-A
+Macromolecule #49: RPL9A isoform 1
+Macromolecule #50: RPL10 isoform 1
+Macromolecule #51: RPL11B isoform 1
+Macromolecule #52: 60S ribosomal protein L13-A
+Macromolecule #53: 60S ribosomal protein L14-A
+Macromolecule #54: 60S ribosomal protein L15-A
+Macromolecule #55: 60S ribosomal protein L16-A
+Macromolecule #56: 60S ribosomal protein L17-A
+Macromolecule #57: 60S ribosomal protein L19-A
+Macromolecule #58: 60S ribosomal protein L20-A
+Macromolecule #59: 60S ribosomal protein L21-A
+Macromolecule #60: 60S ribosomal protein L22-A
+Macromolecule #61: 60S ribosomal protein L24-A
+Macromolecule #62: 60S ribosomal protein L25
+Macromolecule #63: 60S ribosomal protein L26-A
+Macromolecule #64: 60S ribosomal protein L27-A
+Macromolecule #65: 60S ribosomal protein L28
+Macromolecule #66: 60S ribosomal protein L29
+Macromolecule #67: 60S ribosomal protein L30
+Macromolecule #68: RPL32 isoform 1
+Macromolecule #69: 60S ribosomal protein L33-A
+Macromolecule #70: 60S ribosomal protein L34-A
+Macromolecule #71: 60S ribosomal protein L35-A
+Macromolecule #72: 60S ribosomal protein L37-A
+Macromolecule #73: RPL38 isoform 1
+Macromolecule #74: 60S ribosomal protein L39
+Macromolecule #75: 60S ribosomal protein L40-A
+Macromolecule #76: 60S ribosomal protein L41
+Macromolecule #77: 60S ribosomal protein L42-A
+Macromolecule #78: 60S ribosomal protein L43-A
+Macromolecule #79: Methionine aminopeptidase 1
+Macromolecule #80: 60S ribosomal protein L1-A
+Macromolecule #33: 18S rRNA
+Macromolecule #41: 25S rRNA
+Macromolecule #42: 5S rRNA
+Macromolecule #43: 5.8S rRNA
+Macromolecule #81: ZINC ION
-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 | FEI TITAN KRIOS |
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| Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.16 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: 3.2 µm / Nominal defocus min: 0.5 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi




Keywords
Authors
Germany, 1 items
Citation
















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Processing
FIELD EMISSION GUN


