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- PDB-8oo0: Chaetomium thermophilum Methionine Aminopeptidase 2 autoproteolys... -

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Basic information

Entry
Database: PDB / ID: 8oo0
TitleChaetomium thermophilum Methionine Aminopeptidase 2 autoproteolysis product at the 80S ribosome
Components
  • (40S ribosomal protein ...) x 30
  • (60S ribosomal protein ...) x 32
  • (Putative 60S ribosomal ...) x 2
  • (Putative ribosomal ...) x 2
  • (Ribosomal protein ...) x 7
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • 60S acidic ribosomal protein P0
  • Hyaluronan/mRNA-binding protein domain-containing protein
  • Methionine aminopeptidase 2
  • Putative guanine nucleotide-binding protein
  • Ribosome-associated molecular chaperone SSB1
  • Ubiquitin-like domain-containing protein
  • dolichyl-diphosphooligosaccharide--protein glycotransferase
KeywordsMETAL 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
Function and homology information


dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / preribosome / protein N-linked glycosylation via asparagine / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / protein kinase regulator activity / metalloaminopeptidase activity / non-chaperonin molecular chaperone ATPase / 90S preribosome ...dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / preribosome / protein N-linked glycosylation via asparagine / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / protein kinase regulator activity / metalloaminopeptidase activity / non-chaperonin molecular chaperone ATPase / 90S preribosome / protein-RNA complex assembly / translation regulator activity / endomembrane system / post-translational protein modification / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / methyltransferase activity / maturation of SSU-rRNA / small-subunit processome / ATP-dependent protein folding chaperone / rRNA processing / ribosome biogenesis / large ribosomal subunit / regulation of translation / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / methylation / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Gcn1, N-terminal / : / : / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / Stalled ribosome sensor GCN1-like, HEAT repeats / Fungal GCN1-like, HEAT repeats / Stalled ribosome sensor GCN1 N-terminal / Hyaluronan / mRNA binding family / E-Z type HEAT repeats / PBS lyase HEAT-like repeat ...Gcn1, N-terminal / : / : / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / Stalled ribosome sensor GCN1-like, HEAT repeats / Fungal GCN1-like, HEAT repeats / Stalled ribosome sensor GCN1 N-terminal / Hyaluronan / mRNA binding family / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Elongation factor 3/GNC1 HEAT repeat / EF3 N-terminal HEAT repeat / Centrosomal protein CEP104-like, TOG domain / Peptidase M24A, methionine aminopeptidase, subfamily 2 / : / RNA binding protein HABP4/SERBP1 / : / STT3/PglB/AglB core domain / Stm1-like, N-terminal / Stm1 / Parkin co-regulated protein / TOG domain / Parkin co-regulated protein / TOG / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / Peptidase M24, methionine aminopeptidase / HEAT repeat profile. / HEAT, type 2 / 60s Acidic ribosomal protein / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / 60S acidic ribosomal protein P0 / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / : / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Ribosomal protein L30e / Ribosomal protein L28e / 50S ribosomal protein L10, insertion domain superfamily / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L19e, C-terminal domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S5, eukaryotic/archaeal / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / S27a-like superfamily / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e / 40S Ribosomal protein S10 / : / Ribosomal protein L44e signature. / Ribosomal protein S7e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19/L19e conserved site
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ubiquitin-like domain-containing protein / Large ribosomal subunit protein uL3 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ubiquitin-like domain-containing protein / Large ribosomal subunit protein uL3 / 40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / Small ribosomal subunit protein uS2 / 60S ribosomal protein L26-like protein / Ribosomal protein L15 / 40S ribosomal protein s10-like protein / 60S ribosomal protein L27 / 40S ribosomal protein S13-like protein / 40S ribosomal protein s15-like protein / 60S ribosomal protein L6 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 / 60S ribosomal protein l9-like protein / 60S ribosomal protein l21-like protein / 40S ribosomal protein s9-like protein / Ribosomal protein L37 / 40S ribosomal protein S4 / 60S ribosomal protein L14-like protein / Ribosomal protein s27-like protein / 40S ribosomal protein S25 / 40S ribosomal protein s5-like protein / 40S ribosomal protein S26 / 40S ribosomal protein S27a-like protein / 40S ribosomal protein S20-like protein / Hyaluronan/mRNA-binding protein domain-containing protein / 60S ribosomal protein L2-like protein / 60S ribosomal protein L25-like protein / 60S ribosomal protein L43-like protein / 40S ribosomal protein S3 / Putative ribosomal protein / 60S ribosomal protein L32-like protein / Small ribosomal subunit protein eS1 / 40S ribosomal protein S17-like protein / 40S ribosomal protein S7 / 60S ribosomal protein L13 / Ribosomal protein L18-like protein / 40S ribosomal protein S28-like protein / Ribosomal protein L19 / Putative guanine nucleotide-binding protein / 60S ribosomal protein L8 / Small ribosomal subunit protein uS5 / 60S ribosomal protein L36 / 40S ribosomal protein S16-like protein / 60S ribosomal protein L44-like protein / 60S ribosomal protein L20 / 60S ribosomal protein l33-like protein / Ribosome-associated molecular chaperone SSB1 / Putative 60S ribosomal protein / 60S ribosomal protein L22-like protein / Methionine aminopeptidase 2 / Large ribosomal subunit protein uL18 / 60S ribosomal protein l30-like protein / 60S ribosomal protein L10-like protein / 40S ribosomal protein S11-like protein / 60S ribosomal protein L4-like protein / 40S ribosomal protein S19-like protein / 60S ribosomal protein l7-like protein / 40S ribosomal protein S14-like protein / Ribosomal protein l34-like protein / 60S ribosomal protein L12-like protein / 60S acidic ribosomal protein P0 / Large ribosomal subunit protein uL22 / 60S ribosomal protein L16-like protein / 40S ribosomal protein S12 / 40S ribosomal protein S22-like protein / Putative 60S ribosomal protein / Large ribosomal subunit protein uL5 / 40S ribosomal protein S21-like protein / 60S ribosomal protein l23-like protein / Large ribosomal subunit protein eL24-related N-terminal domain-containing protein / Ribosomal protein L38e / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS32A / 40S ribosomal protein S30 / Large ribosomal subunit protein eL39 / 60S ribosomal protein L29 / 40S ribosomal protein S29
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
Thermochaetoides thermophila (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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
1: 28S rRNA
2: 18S rRNA
3: 5S rRNA
4: 5.8S rRNA
A: Putative guanine nucleotide-binding protein
B: Hyaluronan/mRNA-binding protein domain-containing protein
C: Ribosome-associated molecular chaperone SSB1
LA: 60S ribosomal protein L2-like protein
LB: 60S ribosomal protein L3-like protein
LC: 60S ribosomal protein L4-like protein
LD: 60S ribosomal protein l5-like protein
LE: 60S ribosomal protein L6
LF: 60S ribosomal protein l7-like protein
LG: 60S ribosomal protein L8
LH: 60S ribosomal protein l9-like protein
LI: 60S ribosomal protein L10-like protein
LJ: Putative ribosomal protein
LK: 60S ribosomal protein L12-like protein
LL: 60S ribosomal protein L13
LM: 60S ribosomal protein L14-like protein
LN: Ribosomal protein L15
LO: 60S ribosomal protein L16-like protein
LP: 60S ribosomal protein l17-like protein
LQ: Ribosomal protein L18-like protein
LR: Ribosomal protein L19
LS: 60S ribosomal protein L20
LT: 60S ribosomal protein l21-like protein
LU: 60S ribosomal protein L22-like protein
LV: 60S ribosomal protein l23-like protein
LW: 60S ribosomal protein L24
LX: 60S ribosomal protein L25-like protein
LY: 60S ribosomal protein L26-like protein
LZ: 60S ribosomal protein L27
La: Ribosomal protein L18e/L15P domain-containing protein
Lb: 60S ribosomal protein L29
Lc: 60S ribosomal protein l30-like protein
Ld: Putative 60S ribosomal protein
Le: 60S ribosomal protein L32-like protein
Lf: 60S ribosomal protein l33-like protein
Lg: Ribosomal protein l34-like protein
Lh: dolichyl-diphosphooligosaccharide--protein glycotransferase
Li: 60S ribosomal protein L36
Lj: Ribosomal protein L37
Lk: 60S ribosomal protein L38
Ll: 60S ribosomal protein L39
Lm: Ubiquitin-like domain-containing protein
Ln: 60S ribosomal protein L41-A
Lo: 60S ribosomal protein L44-like protein
Lp: 60S ribosomal protein L43-like protein
Lq: Putative 60S ribosomal protein
Lr: 60S ribosomal protein L41-A
Ls: 60S acidic ribosomal protein P0
SA: 40S ribosomal protein S0
SB: 40S ribosomal protein S1
SC: 40S ribosomal protein S2-like protein
SD: 40S ribosomal protein S3-like protein
SE: 40S ribosomal protein S4
SF: 40S ribosomal protein s5-like protein
SG: 40S ribosomal protein S6
SH: 40S ribosomal protein S7
SI: 40S ribosomal protein S8
SJ: 40S ribosomal protein s9-like protein
SK: 40S ribosomal protein s10-like protein
SL: 40S ribosomal protein S11-like protein
SM: 40S ribosomal protein S12
SN: 40S ribosomal protein S13-like protein
SO: 40S ribosomal protein S14-like protein
SP: 40S ribosomal protein s15-like protein
SQ: 40S ribosomal protein S16-like protein
SR: 40S ribosomal protein S17-like protein
SS: Putative ribosomal protein
ST: 40S ribosomal protein S19-like protein
SU: 40S ribosomal protein S20-like protein
SV: 40S ribosomal protein S21-like protein
SW: 40S ribosomal protein S22-like protein
SX: 40S ribosomal protein s23-like protein
SY: 40S ribosomal protein S24
SZ: 40S ribosomal protein S25
Sa: 40S ribosomal protein S26
Sb: Ribosomal protein s27-like protein
Sc: 40S ribosomal protein S28-like protein
Sd: 40S ribosomal protein S29
Se: 40S ribosomal protein S30
Sf: 40S ribosomal protein S27a-like protein
D: Methionine aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,341,84393
Polymers3,341,32085
Non-polymers5238
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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RNA chain , 4 types, 4 molecules 1234

#1: RNA chain 28S rRNA


Mass: 1078730.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: GenBank: 7OLC_1
#2: RNA chain 18S rRNA


Mass: 578887.625 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: 7OLC_2
#3: RNA chain 5S rRNA


Mass: 38596.891 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: 7OLC_3
#4: 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 (fungus) / References: GenBank: MT316345.1

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Protein , 7 types, 7 molecules ABCLhLmLsD

#5: Protein Putative guanine nucleotide-binding protein


Mass: 35149.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S9U0
#6: Protein Hyaluronan/mRNA-binding protein domain-containing protein


Mass: 32667.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S428
#7: Protein Ribosome-associated molecular chaperone SSB1 / Heat shock protein SSB1 / Hsp70 chaperone Ssb


Mass: 67110.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus)
References: UniProt: G0SCU5, non-chaperonin molecular chaperone ATPase
#41: Protein dolichyl-diphosphooligosaccharide--protein glycotransferase


Mass: 14643.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus)
References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase
#46: Protein Ubiquitin-like domain-containing protein


Mass: 14609.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: A0A2A9PNA8
#51: Protein 60S acidic ribosomal protein P0


Mass: 33853.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SGP3
#84: Protein Methionine aminopeptidase 2


Mass: 41310.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0063100 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0SEA9

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60S ribosomal protein ... , 32 types, 33 molecules LALBLCLDLELFLGLHLILKLLLMLOLPLSLTLULVLWLXLYLZLbLcLeLfLiLkLlLn...

#8: Protein 60S ribosomal protein L2-like protein


Mass: 27598.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S4P8
#9: Protein 60S ribosomal protein L3-like protein


Mass: 44069.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RXW1
#10: Protein 60S ribosomal protein L4-like protein


Mass: 39439.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SFC3
#11: Protein 60S ribosomal protein l5-like protein


Mass: 35034.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SEG2
#12: Protein 60S ribosomal protein L6


Mass: 22132.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S0D6
#13: Protein 60S ribosomal protein l7-like protein


Mass: 28821.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SFL0
#14: Protein 60S ribosomal protein L8


Mass: 29744.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SAJ9
#15: Protein 60S ribosomal protein l9-like protein


Mass: 21582.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S0E5
#16: Protein 60S ribosomal protein L10-like protein


Mass: 25255.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SEI1
#18: Protein 60S ribosomal protein L12-like protein


Mass: 17802.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SGH8
#19: Protein 60S ribosomal protein L13


Mass: 24191.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S992
#20: Protein 60S ribosomal protein L14-like protein


Mass: 16111.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S1R0
#22: Protein 60S ribosomal protein L16-like protein


Mass: 23035.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SH61
#23: Protein 60S ribosomal protein l17-like protein


Mass: 20941.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SGY1
#26: Protein 60S ribosomal protein L20


Mass: 20341.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SCE2
#27: Protein 60S ribosomal protein l21-like protein


Mass: 18159.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S0Z3
#28: Protein 60S ribosomal protein L22-like protein


Mass: 14302.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SDS8
#29: Protein 60S ribosomal protein l23-like protein


Mass: 14674.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SI44
#30: Protein 60S ribosomal protein L24


Mass: 18081.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G2Q623
#31: Protein 60S ribosomal protein L25-like protein


Mass: 17175.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S507
#32: Protein 60S ribosomal protein L26-like protein


Mass: 15565.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RYN9
#33: Protein 60S ribosomal protein L27


Mass: 15803.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RZE9
#35: Protein 60S ribosomal protein L29


Mass: 7529.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: Q2H9W4
#36: Protein 60S ribosomal protein l30-like protein


Mass: 11602.616 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SEI0
#38: Protein 60S ribosomal protein L32-like protein


Mass: 15095.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S6V4
#39: Protein 60S ribosomal protein l33-like protein


Mass: 12330.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SCL3
#42: Protein 60S ribosomal protein L36


Mass: 12784.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SBN1
#44: Protein 60S ribosomal protein L38


Mass: 9466.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G2Q8J4
#45: Protein 60S ribosomal protein L39


Mass: 6297.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: Q2H9R2
#47: Protein/peptide 60S ribosomal protein L41-A / L47 / Large ribosomal subunit protein eL41-A / YL41


Mass: 3354.243 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: P0CX86
#48: Protein 60S ribosomal protein L44-like protein


Mass: 12045.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SBZ6
#49: Protein 60S ribosomal protein L43-like protein


Mass: 10158.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S6B0

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Putative ribosomal ... , 2 types, 2 molecules LJSS

#17: Protein Putative ribosomal protein


Mass: 20119.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SHQ2
#70: Protein Putative ribosomal protein


Mass: 17826.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S6J7

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Ribosomal protein ... , 7 types, 7 molecules LNLQLRLaLgLjSb

#21: Protein Ribosomal protein L15


Mass: 24307.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RZ88
#24: Protein Ribosomal protein L18-like protein


Mass: 24195.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S9B5
#25: Protein Ribosomal protein L19


Mass: 22409.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S9T3
#34: Protein Ribosomal protein L18e/L15P domain-containing protein


Mass: 16848.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G2QB77
#40: Protein Ribosomal protein l34-like protein


Mass: 13492.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SFN0
#43: Protein Ribosomal protein L37


Mass: 10660.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S101
#79: Protein Ribosomal protein s27-like protein


Mass: 8923.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S1S4

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Putative 60S ribosomal ... , 2 types, 2 molecules LdLq

#37: Protein Putative 60S ribosomal protein


Mass: 13872.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SD68
#50: Protein Putative 60S ribosomal protein


Mass: 15960.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SHJ6

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40S ribosomal protein ... , 30 types, 30 molecules SASBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSTSUSVSWSXSYSZSaScSdSeSf

#52: Protein 40S ribosomal protein S0


Mass: 31158.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RYF9
#53: Protein 40S ribosomal protein S1


Mass: 29245.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S7T8
#54: Protein 40S ribosomal protein S2-like protein


Mass: 28556.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SAV4
#55: Protein 40S ribosomal protein S3-like protein


Mass: 27893.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S6I7
#56: Protein 40S ribosomal protein S4


Mass: 29800.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S1A6
#57: Protein 40S ribosomal protein s5-like protein


Mass: 23679.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S1Z0
#58: Protein 40S ribosomal protein S6


Mass: 27490.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RY43
#59: Protein 40S ribosomal protein S7


Mass: 23084.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S8C4
#60: Protein 40S ribosomal protein S8


Mass: 23102.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RY45
#61: Protein 40S ribosomal protein s9-like protein


Mass: 22029.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S0Z4
#62: Protein 40S ribosomal protein s10-like protein


Mass: 18121.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RZD8
#63: Protein 40S ribosomal protein S11-like protein


Mass: 18698.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SF00
#64: Protein 40S ribosomal protein S12


Mass: 15961.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SHH9
#65: Protein 40S ribosomal protein S13-like protein


Mass: 16912.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RZM9
#66: Protein 40S ribosomal protein S14-like protein


Mass: 16071.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SFL1
#67: Protein 40S ribosomal protein s15-like protein


Mass: 17601.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S084
#68: Protein 40S ribosomal protein S16-like protein


Mass: 15962.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SBR7
#69: Protein 40S ribosomal protein S17-like protein


Mass: 16720.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S871
#71: Protein 40S ribosomal protein S19-like protein


Mass: 17151.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SFK8
#72: Protein 40S ribosomal protein S20-like protein


Mass: 13212.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S379
#73: Protein 40S ribosomal protein S21-like protein


Mass: 10961.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SI21
#74: Protein 40S ribosomal protein S22-like protein


Mass: 14905.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SHI0
#75: Protein 40S ribosomal protein s23-like protein


Mass: 15934.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RY17
#76: Protein 40S ribosomal protein S24


Mass: 15535.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: P0CU28
#77: Protein 40S ribosomal protein S25


Mass: 10932.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S1Y9
#78: Protein 40S ribosomal protein S26


Mass: 13616.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S2X4
#80: Protein 40S ribosomal protein S28-like protein


Mass: 7741.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S9M9
#81: Protein 40S ribosomal protein S29


Mass: 6504.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: Q2HB68
#82: Protein 40S ribosomal protein S30


Mass: 6793.089 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: Q2H4C5
#83: Protein 40S ribosomal protein S27a-like protein


Mass: 17731.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S2X5

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Non-polymers , 1 types, 8 molecules

#85: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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 autoproteolysis product in complex with the 80S ribosome
Type: COMPLEX / Entity ID: #1-#84 / 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: 54.8 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119160 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 108.07 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0055223721
ELECTRON MICROSCOPYf_angle_d0.6139327371
ELECTRON MICROSCOPYf_chiral_restr0.041140727
ELECTRON MICROSCOPYf_plane_restr0.006922176
ELECTRON MICROSCOPYf_dihedral_angle_d14.9764101226

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