+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16191 | |||||||||
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Title | Yeast 80S ribosome in complex with Map1 (conformation 2) | |||||||||
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 / initiator methionyl aminopeptidase activity / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling ...Inactivation, recovery and regulation of the phototransduction cascade / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / pre-mRNA 5'-splice site binding / preribosome, small subunit precursor / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / response to cycloheximide / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / metalloaminopeptidase 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 / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / regulation of amino acid metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / G-protein alpha-subunit binding / positive regulation of protein kinase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / protein-RNA complex assembly / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA / cytosolic ribosome / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / 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 / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / maintenance of translational fidelity / protein processing / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / protein ubiquitination / translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / 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: 3.8 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_16191.map.gz | 244.2 MB | EMDB map data format | |
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Header (meta data) | emd-16191-v30.xml emd-16191.xml | 89.3 KB 89.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16191_fsc.xml | 14.9 KB | Display | FSC data file |
Images | emd_16191.png | 133.8 KB | ||
Others | emd_16191_half_map_1.map.gz emd_16191_half_map_2.map.gz | 226.5 MB 225.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16191 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16191 | HTTPS FTP |
-Validation report
Summary document | emd_16191_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_16191_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_16191_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | emd_16191_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16191 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16191 | HTTPS FTP |
-Related structure data
Related structure data | 8bqxMC 8bipC 8bjqC 8bqdC 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_16191.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 | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_16191_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16191_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: Methionine aminopeptidase 1
+Macromolecule #2: 40S ribosomal protein S3
+Macromolecule #3: 40S ribosomal protein S5
+Macromolecule #4: 40S ribosomal protein S10-A
+Macromolecule #5: 40S ribosomal protein S12
+Macromolecule #6: 40S ribosomal protein S15
+Macromolecule #7: 40S ribosomal protein S16-A
+Macromolecule #8: 40S ribosomal protein S17-A
+Macromolecule #9: 40S ribosomal protein S18-A
+Macromolecule #10: 40S ribosomal protein S19-A
+Macromolecule #11: 40S ribosomal protein S20
+Macromolecule #12: 40S ribosomal protein S25-A
+Macromolecule #13: 40S ribosomal protein S28-A
+Macromolecule #14: 40S ribosomal protein S29-A
+Macromolecule #15: 40S ribosomal protein S31
+Macromolecule #16: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #17: 40S ribosomal protein S0-A
+Macromolecule #18: 40S ribosomal protein S1-A
+Macromolecule #19: 40S ribosomal protein S2
+Macromolecule #20: 40S ribosomal protein S4-A
+Macromolecule #21: 40S ribosomal protein S6-A
+Macromolecule #22: 40S ribosomal protein S7-A
+Macromolecule #23: 40S ribosomal protein S8-A
+Macromolecule #24: 40S ribosomal protein S9-A
+Macromolecule #25: 40S ribosomal protein S11-A
+Macromolecule #26: 40S ribosomal protein S13
+Macromolecule #27: 40S ribosomal protein S14-B
+Macromolecule #28: 60S ribosomal protein L8-A
+Macromolecule #29: 60S ribosomal protein L3
+Macromolecule #30: 60S ribosomal protein L23-A
+Macromolecule #31: 60S ribosomal protein L18-A
+Macromolecule #32: 60S ribosomal protein L36-A
+Macromolecule #33: 60S ribosomal protein L31-A
+Macromolecule #35: 40S ribosomal protein S21-A
+Macromolecule #36: 40S ribosomal protein S22-A
+Macromolecule #37: 40S ribosomal protein S23-A
+Macromolecule #38: 40S ribosomal protein S24-A
+Macromolecule #39: 40S ribosomal protein S26-B
+Macromolecule #40: 40S ribosomal protein S27-A
+Macromolecule #41: 40S ribosomal protein S30-A
+Macromolecule #45: 60S ribosomal protein L2-A
+Macromolecule #46: 60S ribosomal protein L4-A
+Macromolecule #47: 60S ribosomal protein L5
+Macromolecule #48: 60S ribosomal protein L6-B
+Macromolecule #49: 60S ribosomal protein L7-A
+Macromolecule #50: 60S ribosomal protein L9-A
+Macromolecule #51: RPL10 isoform 1
+Macromolecule #52: RPL11B isoform 1
+Macromolecule #53: 60S ribosomal protein L13-A
+Macromolecule #54: 60S ribosomal protein L14-A
+Macromolecule #55: 60S ribosomal protein L15-A
+Macromolecule #56: 60S ribosomal protein L16-A
+Macromolecule #57: 60S ribosomal protein L17-A
+Macromolecule #58: 60S ribosomal protein L19-A
+Macromolecule #59: 60S ribosomal protein L20-A
+Macromolecule #60: 60S ribosomal protein L21-A
+Macromolecule #61: 60S ribosomal protein L22-A
+Macromolecule #62: 60S ribosomal protein L24-A
+Macromolecule #63: 60S ribosomal protein L25
+Macromolecule #64: 60S ribosomal protein L26-A
+Macromolecule #65: 60S ribosomal protein L27-A
+Macromolecule #66: 60S ribosomal protein L28
+Macromolecule #67: 60S ribosomal protein L29
+Macromolecule #68: 60S ribosomal protein L30
+Macromolecule #69: RPL32 isoform 1
+Macromolecule #70: 60S ribosomal protein L33-A
+Macromolecule #71: 60S ribosomal protein L34-A
+Macromolecule #72: 60S ribosomal protein L35-A
+Macromolecule #73: 60S ribosomal protein L37-A
+Macromolecule #74: RPL38 isoform 1
+Macromolecule #75: 60S ribosomal protein L39
+Macromolecule #76: 60S ribosomal protein L40-A
+Macromolecule #77: 60S ribosomal protein L41-A
+Macromolecule #78: 60S ribosomal protein L42-A
+Macromolecule #79: 60S ribosomal protein L43-A
+Macromolecule #80: 60S ribosomal protein L1-A
+Macromolecule #34: 18S rRNA
+Macromolecule #42: 25S rRNA
+Macromolecule #43: 5S rRNA
+Macromolecule #44: 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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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 |