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Yorodumi- EMDB-17004: Chaetomium thermophilum Methionine Aminopeptidase 2 autoproteolys... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17004 | |||||||||
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Title | Chaetomium thermophilum Methionine Aminopeptidase 2 autoproteolysis product at the 80S ribosome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Ribosome Associated Factor / Protease / A-site / Factor binding site / Decoding center / Protein Maturation / Proteostasis / NME / p67 / p26 / Autoproteolysis / MAP / MetAP / MAP2 / MetAP2 / METAL BINDING PROTEIN | |||||||||
Function / homology | Function and homology information dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / protein kinase regulator activity / non-chaperonin molecular chaperone ATPase / metalloaminopeptidase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome ...dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / protein kinase regulator activity / non-chaperonin molecular chaperone ATPase / metalloaminopeptidase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / post-translational protein modification / 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) / maturation of LSU-rRNA / cellular response to amino acid starvation / rescue of stalled ribosome / 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) / ribosomal large subunit biogenesis / methyltransferase activity / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / ATP-dependent protein folding chaperone / rRNA processing / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / methylation / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / mRNA binding / nucleolus / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermochaetoides thermophila (fungus) / Thermochaetoides thermophila DSM 1495 (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Klein MA / Wild K / Kisonaite M / Sinning I | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Methionine aminopeptidase 2 and its autoproteolysis product have different binding sites on the ribosome. Authors: Marius A Klein / Klemens Wild / Miglė Kišonaitė / Irmgard Sinning / Abstract: Excision of the initiator methionine is among the first co-translational processes that occur at the ribosome. While this crucial step in protein maturation is executed by two types of methionine ...Excision of the initiator methionine is among the first co-translational processes that occur at the ribosome. While this crucial step in protein maturation is executed by two types of methionine aminopeptidases in eukaryotes (MAP1 and MAP2), additional roles in disease and translational regulation have drawn more attention to MAP2. Here, we report several cryo-EM structures of human and fungal MAP2 at the 80S ribosome. Irrespective of nascent chains, MAP2 can occupy the tunnel exit. On nascent chain displaying ribosomes, the MAP2-80S interaction is highly dynamic and the MAP2-specific N-terminal extension engages in stabilizing interactions with the long rRNA expansion segment ES27L. Loss of this extension by autoproteolytic cleavage impedes interactions at the tunnel, while promoting MAP2 to enter the ribosomal A-site, where it engages with crucial functional centers of translation. These findings reveal that proteolytic remodeling of MAP2 severely affects ribosome binding, and set the stage for targeted functional studies. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17004.map.gz | 414.4 MB | EMDB map data format | |
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Header (meta data) | emd-17004-v30.xml emd-17004.xml | 104 KB 104 KB | Display Display | EMDB header |
Images | emd_17004.png | 79.5 KB | ||
Filedesc metadata | emd-17004.cif.gz | 20.6 KB | ||
Others | emd_17004_half_map_1.map.gz emd_17004_half_map_2.map.gz | 700.8 MB 700.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17004 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17004 | HTTPS FTP |
-Validation report
Summary document | emd_17004_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_17004_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_17004_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | emd_17004_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17004 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17004 | HTTPS FTP |
-Related structure data
Related structure data | 8oo0MC 8onxC 8onyC 8onzC 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_17004.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.11 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_17004_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17004_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : MAP2 autoproteolysis product in complex with the 80S ribosome
+Supramolecule #1: MAP2 autoproteolysis product in complex with the 80S ribosome
+Macromolecule #1: 28S rRNA
+Macromolecule #2: 18S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #4: 5.8S rRNA
+Macromolecule #5: Putative guanine nucleotide-binding protein
+Macromolecule #6: Hyaluronan/mRNA-binding protein domain-containing protein
+Macromolecule #7: Ribosome-associated molecular chaperone SSB1
+Macromolecule #8: 60S ribosomal protein L2-like protein
+Macromolecule #9: 60S ribosomal protein L3-like protein
+Macromolecule #10: 60S ribosomal protein L4-like protein
+Macromolecule #11: 60S ribosomal protein l5-like protein
+Macromolecule #12: 60S ribosomal protein L6
+Macromolecule #13: 60S ribosomal protein l7-like protein
+Macromolecule #14: 60S ribosomal protein L8
+Macromolecule #15: 60S ribosomal protein l9-like protein
+Macromolecule #16: 60S ribosomal protein L10-like protein
+Macromolecule #17: Putative ribosomal protein
+Macromolecule #18: 60S ribosomal protein L12-like protein
+Macromolecule #19: 60S ribosomal protein L13
+Macromolecule #20: 60S ribosomal protein L14-like protein
+Macromolecule #21: Ribosomal protein L15
+Macromolecule #22: 60S ribosomal protein L16-like protein
+Macromolecule #23: 60S ribosomal protein l17-like protein
+Macromolecule #24: Ribosomal protein L18-like protein
+Macromolecule #25: Ribosomal protein L19
+Macromolecule #26: 60S ribosomal protein L20
+Macromolecule #27: 60S ribosomal protein l21-like protein
+Macromolecule #28: 60S ribosomal protein L22-like protein
+Macromolecule #29: 60S ribosomal protein l23-like protein
+Macromolecule #30: 60S ribosomal protein L24
+Macromolecule #31: 60S ribosomal protein L25-like protein
+Macromolecule #32: 60S ribosomal protein L26-like protein
+Macromolecule #33: 60S ribosomal protein L27
+Macromolecule #34: Ribosomal protein L18e/L15P domain-containing protein
+Macromolecule #35: 60S ribosomal protein L29
+Macromolecule #36: 60S ribosomal protein l30-like protein
+Macromolecule #37: Putative 60S ribosomal protein
+Macromolecule #38: 60S ribosomal protein L32-like protein
+Macromolecule #39: 60S ribosomal protein l33-like protein
+Macromolecule #40: Ribosomal protein l34-like protein
+Macromolecule #41: dolichyl-diphosphooligosaccharide--protein glycotransferase
+Macromolecule #42: 60S ribosomal protein L36
+Macromolecule #43: Ribosomal protein L37
+Macromolecule #44: 60S ribosomal protein L38
+Macromolecule #45: 60S ribosomal protein L39
+Macromolecule #46: Ubiquitin-like domain-containing protein
+Macromolecule #47: 60S ribosomal protein L41-A
+Macromolecule #48: 60S ribosomal protein L44-like protein
+Macromolecule #49: 60S ribosomal protein L43-like protein
+Macromolecule #50: Putative 60S ribosomal protein
+Macromolecule #51: 60S acidic ribosomal protein P0
+Macromolecule #52: 40S ribosomal protein S0
+Macromolecule #53: 40S ribosomal protein S1
+Macromolecule #54: 40S ribosomal protein S2-like protein
+Macromolecule #55: 40S ribosomal protein S3-like protein
+Macromolecule #56: 40S ribosomal protein S4
+Macromolecule #57: 40S ribosomal protein s5-like protein
+Macromolecule #58: 40S ribosomal protein S6
+Macromolecule #59: 40S ribosomal protein S7
+Macromolecule #60: 40S ribosomal protein S8
+Macromolecule #61: 40S ribosomal protein s9-like protein
+Macromolecule #62: 40S ribosomal protein s10-like protein
+Macromolecule #63: 40S ribosomal protein S11-like protein
+Macromolecule #64: 40S ribosomal protein S12
+Macromolecule #65: 40S ribosomal protein S13-like protein
+Macromolecule #66: 40S ribosomal protein S14-like protein
+Macromolecule #67: 40S ribosomal protein s15-like protein
+Macromolecule #68: 40S ribosomal protein S16-like protein
+Macromolecule #69: 40S ribosomal protein S17-like protein
+Macromolecule #70: Putative ribosomal protein
+Macromolecule #71: 40S ribosomal protein S19-like protein
+Macromolecule #72: 40S ribosomal protein S20-like protein
+Macromolecule #73: 40S ribosomal protein S21-like protein
+Macromolecule #74: 40S ribosomal protein S22-like protein
+Macromolecule #75: 40S ribosomal protein s23-like protein
+Macromolecule #76: 40S ribosomal protein S24
+Macromolecule #77: 40S ribosomal protein S25
+Macromolecule #78: 40S ribosomal protein S26
+Macromolecule #79: Ribosomal protein s27-like protein
+Macromolecule #80: 40S ribosomal protein S28-like protein
+Macromolecule #81: 40S ribosomal protein S29
+Macromolecule #82: 40S ribosomal protein S30
+Macromolecule #83: 40S ribosomal protein S27a-like protein
+Macromolecule #84: Methionine aminopeptidase 2
+Macromolecule #85: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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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 QUANTUM (4k x 4k) / Average electron dose: 54.8 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: 2.1 µm / Nominal defocus min: 1.1 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119160 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |