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- PDB-8oo0: Chaetomium thermophilum Methionine Aminopeptidase 2 autoproteolys... -
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Basic information
Entry | Database: PDB / ID: 8oo0 | ||||||
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Title | Chaetomium thermophilum Methionine Aminopeptidase 2 autoproteolysis product at the 80S ribosome | ||||||
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![]() | METAL BINDING PROTEIN / Ribosome Associated Factor / Protease / A-site / Factor binding site / Decoding center / Protein Maturation / Proteostasis / NME / p67 / p26 / Autoproteolysis / MAP / MetAP / MAP2 / MetAP2 | ||||||
Function / homology | ![]() 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 / 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) / post-translational protein modification / 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 / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / mRNA binding / nucleolus / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
![]() | Klein, M.A. / Wild, K. / Kisonaite, M. / Sinning, I. | ||||||
Funding support | ![]()
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![]() | ![]() 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
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 4.6 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 17004MC ![]() 8onxC ![]() 8onyC ![]() 8onzC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 4 types, 4 molecules 1234
#1: RNA chain | Mass: 1078730.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: RNA chain | Mass: 578887.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: GenBank: 7OLC_2 |
#3: RNA chain | Mass: 38596.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: GenBank: 7OLC_3 |
#4: RNA chain | Mass: 50147.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() |
-Protein , 7 types, 7 molecules ABCLhLmLsD
#5: Protein | Mass: 35149.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#6: Protein | Mass: 32667.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein | Mass: 67110.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: G0SCU5, non-chaperonin molecular chaperone ATPase |
#41: Protein | Mass: 14643.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase |
#46: Protein | Mass: 14609.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#51: Protein | Mass: 33853.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#84: Protein | Mass: 41310.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
+60S ribosomal protein ... , 32 types, 33 molecules LALBLCLDLELFLGLHLILKLLLMLOLPLSLTLULVLWLXLYLZLbLcLeLfLiLkLlLn...
-Putative ribosomal ... , 2 types, 2 molecules LJSS
#17: Protein | Mass: 20119.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#70: Protein | Mass: 17826.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Ribosomal protein ... , 7 types, 7 molecules LNLQLRLaLgLjSb
#21: Protein | Mass: 24307.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#24: Protein | Mass: 24195.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#25: Protein | Mass: 22409.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#34: Protein | Mass: 16848.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#40: Protein | Mass: 13492.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#43: Protein | Mass: 10660.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#79: Protein | Mass: 8923.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Putative 60S ribosomal ... , 2 types, 2 molecules LdLq
#37: Protein | Mass: 13872.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#50: Protein | Mass: 15960.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+40S ribosomal protein ... , 30 types, 30 molecules SASBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSTSUSVSWSXSYSZSaScSdSeSf
-Non-polymers , 1 types, 8 molecules ![](data/chem/img/ZN.gif)
#85: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: MAP2 autoproteolysis product in complex with the 80S ribosome Type: COMPLEX / Entity ID: #1-#84 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 1100 nm |
Image recording | Electron dose: 54.8 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.19_4092 / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119160 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 108.07 Å2 | ||||||||||||||||||||||||
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