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- PDB-8onz: Chaetomium thermophilum Methionine Aminopeptidase 2 at the 80S ri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8onz | ||||||
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Title | Chaetomium thermophilum Methionine Aminopeptidase 2 at the 80S ribosome | ||||||
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![]() | METAL BINDING PROTEIN / Ribosome Associated Factor / ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 488.4 KB | 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 | ![]() 17003MC ![]() 8onxC ![]() 8onyC ![]() 8oo0C 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
-Protein , 3 types, 3 molecules LRLhA
#1: Protein | ![]() Mass: 317092.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CTHT_0047080 Production host: ![]() References: UniProt: G0S9T3 |
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#4: Protein | Mass: 105169.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This protein is wrongly annoted as dolichyl-diphosphooligosaccharide-protein glycotransferase in uniprotKB, which explains the long non-matching C-terminus. Source: (gene. exp.) ![]() Gene: CTHT_0009650 Production host: ![]() References: UniProt: G0S0D7, ![]() |
#8: Protein | ![]() Mass: 48912.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CTHT_0063100 / Production host: ![]() ![]() ![]() |
-60S ribosomal protein ... , 3 types, 3 molecules LXLYLk
#2: Protein | ![]() Mass: 17175.334 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: G0S507 |
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#3: Protein | ![]() Mass: 15565.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: G0RYN9 |
#5: Protein | ![]() Mass: 10902.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CTHT_0065470 Production host: ![]() References: UniProt: G0SG89 |
-RNA chain , 2 types, 2 molecules 12
#6: RNA chain | ![]() Mass: 1078716.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: alignment does not work properly here in context of 28S rRNA sequence ... to be redone Source: (gene. exp.) ![]() Production host: ![]() References: ![]() |
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#7: RNA chain | ![]() Mass: 50147.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: MAP2 at the 80S ribosome / Type: COMPLEX / Entity ID: all / 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![]() ![]() |
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![]() |
Image recording | Electron dose: 42.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k 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: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61734 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.8 Å2 | ||||||||||||||||||||||||
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