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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 rRNA18S ribosomal RNA
  • 28S rRNA28S ribosomal RNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Hyaluronan/mRNA-binding protein domain-containing protein
  • Methionine aminopeptidase 2Methionyl aminopeptidase
  • 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 / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / non-chaperonin molecular chaperone ATPase / metalloaminopeptidase activity / protein glycosylation / translation regulator activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome ...dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / non-chaperonin molecular chaperone ATPase / metalloaminopeptidase activity / protein glycosylation / translation regulator activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / methyltransferase activity / ATP-dependent protein folding chaperone / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome binding / large ribosomal subunit / ribosome biogenesis / cytoplasmic translation / small ribosomal subunit / methylation / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Hyaluronan / mRNA binding family / Gcn1, N-terminal / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / RNA binding protein HABP4/SERBP1 / Centrosomal protein CEP104-like, TOG domain / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Peptidase M24A, methionine aminopeptidase, subfamily 2 / Stm1-like, N-terminal / Stm1 ...Hyaluronan / mRNA binding family / Gcn1, N-terminal / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / RNA binding protein HABP4/SERBP1 / Centrosomal protein CEP104-like, TOG domain / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Peptidase M24A, methionine aminopeptidase, subfamily 2 / Stm1-like, N-terminal / Stm1 / Parkin co-regulated protein / Parkin co-regulated protein / TOG domain / : / STT3/PglB/AglB core domain / TOG / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / : / Methionine aminopeptidase subfamily 2 signature. / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / HEAT-like repeat / 60s Acidic ribosomal protein / HEAT repeat profile. / HEAT, type 2 / Peptidase M24, methionine aminopeptidase / 60S acidic ribosomal protein P0 / Ribosomal protein L30e / Ribosomal protein L28e / 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 / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Ribosomal L28e/Mak16 / Peptidase M24 / Metallopeptidase family M24 / Ribosomal L28e protein family / Creatinase/aminopeptidase-like / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S12e / 50S ribosomal protein L10, insertion domain superfamily / : / Small (40S) ribosomal subunit Asc1/RACK1 / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / S27a-like superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / : / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal L29e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L27e, conserved site / Ribosomal protein S19A/S15e / Ribosomal protein S21e signature. / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / : / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein L24e, conserved site / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L34e, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ubiquitin-like domain-containing protein / 60S ribosomal protein L3-like protein ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ubiquitin-like domain-containing protein / 60S ribosomal protein L3-like protein / 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 glycotransferase / 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 / 40S ribosomal protein S2-like protein / 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 / 60S ribosomal protein l5-like protein / 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 / 60S ribosomal protein l17-like protein / 60S ribosomal protein L16-like protein / 40S ribosomal protein S12 / 40S ribosomal protein S22-like protein / Large ribosomal subunit protein eL28 / Putative ribosomal protein / 40S ribosomal protein S21-like protein / 60S ribosomal protein l23-like protein / TRASH domain-containing protein / Ribosomal protein L38e / Large ribosomal subunit protein uL15/eL18 domain-containing protein / 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
Water0
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 / 28S ribosomal RNA


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 / 18S ribosomal RNA


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 / 5S ribosomal RNA


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 / 5.8S ribosomal RNA


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 / Methionyl aminopeptidase


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome / 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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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 / Ribosome


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

-
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 FIELDBright-field microscopy / 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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