+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16182 | |||||||||
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Title | Yeast 80S ribosome in complex with Map1 (conformation 1)Eukaryotic ribosome | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information : / Inactivation, recovery and regulation of the phototransduction cascade / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / methionyl aminopeptidase / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / mTORC1-mediated signalling / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / GDP-dissociation inhibitor activity ...: / Inactivation, recovery and regulation of the phototransduction cascade / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / methionyl aminopeptidase / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / mTORC1-mediated signalling / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / GDP-dissociation inhibitor activity / : / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / 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) / response to cycloheximide / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / metalloaminopeptidase activity / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translation regulator activity / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 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) / regulation of translational fidelity / positive regulation of protein kinase activity / rescue of stalled ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / cellular response to amino acid starvation / small-subunit processome / cytosolic ribosome / protein kinase C binding / maintenance of translational fidelity / macroautophagy / modification-dependent protein catabolic process / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / protein tag activity / ribosomal small subunit assembly / rRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / ribosome biogenesis / small ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / ribonucleoprotein complex / translation / G protein-coupled receptor signaling pathway / response to antibiotic / negative regulation of gene expression / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast) | |||||||||
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: 2023 Title: 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. | |||||||||
History |
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-Structure visualization
Supplemental images |
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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 | 89.3 KB 89.3 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 | ||
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 |
-Related structure data
Related structure data | 8bqdMC 8bipC 8bjqC 8bqxC 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_16182.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||
Density |
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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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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16182_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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 |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.2 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.16 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |