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- PDB-8onz: Chaetomium thermophilum Methionine Aminopeptidase 2 at the 80S ri... -

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Basic information

Entry
Database: PDB / ID: 8onz
TitleChaetomium thermophilum Methionine Aminopeptidase 2 at the 80S ribosome
Components
  • (60S ribosomal protein ...) x 3
  • 28S rRNA
  • 5.8S rRNA
  • Methionine aminopeptidase 2
  • Ribosomal protein L19
  • dolichyl-diphosphooligosaccharide--protein glycotransferase
KeywordsMETAL BINDING PROTEIN / Ribosome Associated Factor / Protease / Tunnel exit / Protein Maturation / Proteostasis / NME / p67 / MAP / MetAP / MAP2 / MetAP2 / ES27L / PTE
Function / homology
Function and homology information


dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / protein glycosylation / protein-RNA complex assembly / large ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding ...dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / protein glycosylation / protein-RNA complex assembly / large ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / proteolysis / RNA binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Gcn1, N-terminal / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Centrosomal protein CEP104-like, TOG domain / Peptidase M24A, methionine aminopeptidase, subfamily 2 / : / : / STT3/PglB/AglB core domain / Parkin co-regulated protein ...Gcn1, N-terminal / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Centrosomal protein CEP104-like, TOG domain / Peptidase M24A, methionine aminopeptidase, subfamily 2 / : / : / STT3/PglB/AglB core domain / Parkin co-regulated protein / Parkin co-regulated protein / TOG domain / TOG / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / HEAT-like repeat / HEAT repeat profile. / HEAT, type 2 / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal proteins L26 eukaryotic, L24P archaeal / Armadillo-like helical / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L26/L24, KOW domain / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / KOW motif / KOW / Armadillo-type fold / Ribosomal protein L2, domain 2 / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L26-like protein / dolichyl-diphosphooligosaccharide--protein glycotransferase / 60S ribosomal protein L25-like protein / Ribosomal protein L19 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L26-like protein / dolichyl-diphosphooligosaccharide--protein glycotransferase / 60S ribosomal protein L25-like protein / Ribosomal protein L19 / Methionine aminopeptidase 2 / 60S ribosomal protein L38-like protein
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsKlein, M.A. / Wild, K. / Kisonaite, M. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SI 586-6 Germany
CitationJournal: 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
DepositionApr 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
LR: Ribosomal protein L19
LX: 60S ribosomal protein L25-like protein
LY: 60S ribosomal protein L26-like protein
Lh: dolichyl-diphosphooligosaccharide--protein glycotransferase
Lk: 60S ribosomal protein L38-like protein
1: 28S rRNA
2: 5.8S rRNA
A: Methionine aminopeptidase 2


Theoretical massNumber of molelcules
Total (without water)1,643,6818
Polymers1,643,6818
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 3 molecules LRLhA

#1: Protein Ribosomal protein L19


Mass: 317092.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0047080
Production host: Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S9T3
#4: Protein dolichyl-diphosphooligosaccharide--protein glycotransferase


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.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0009650
Production host: Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase
#8: Protein Methionine aminopeptidase 2


Mass: 48912.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0063100 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0SEA9

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60S ribosomal protein ... , 3 types, 3 molecules LXLYLk

#2: Protein 60S ribosomal protein L25-like protein


Mass: 17175.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Production host: Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S507
#3: Protein 60S ribosomal protein L26-like protein


Mass: 15565.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Production host: Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0RYN9
#5: Protein 60S ribosomal protein L38-like protein


Mass: 10902.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0065470
Production host: Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SG89

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RNA chain , 2 types, 2 molecules 12

#6: RNA chain 28S rRNA


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.) Thermochaetoides thermophila DSM 1495 (fungus)
Production host: Thermochaetoides thermophila DSM 1495 (fungus)
References: GenBank: XR_002966752.1
#7: RNA chain 5.8S rRNA


Mass: 50147.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Production host: Thermochaetoides thermophila DSM 1495 (fungus)
References: GenBank: XR_002966750.1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MAP2 at the 80S ribosome / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 42.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19_4092 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61734 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 74.8 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003815947
ELECTRON MICROSCOPYf_angle_d0.743123084
ELECTRON MICROSCOPYf_chiral_restr0.04542851
ELECTRON MICROSCOPYf_plane_restr0.0071715
ELECTRON MICROSCOPYf_dihedral_angle_d15.74275021

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