8OO0

Chaetomium thermophilum Methionine Aminopeptidase 2 autoproteolysis product at the 80S ribosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Methionine aminopeptidase 2 and its autoproteolysis product have different binding sites on the ribosome.

Klein, M.A., Wild, K., Kisonaite, M., Sinning, I.

(2024) Nat Commun 15: 716-716

  • DOI: https://doi.org/10.1038/s41467-024-44862-7
  • Primary Citation of Related Structures:  
    8ONX, 8ONY, 8ONZ, 8OO0

  • PubMed 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 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.

    • Organizational Affiliation: 

    Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Putative guanine nucleotide-binding proteinE [auth A]316Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Hyaluronan/mRNA-binding protein domain-containing proteinF [auth B]302Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome-associated molecular chaperone SSB1G [auth C]614Thermochaetoides thermophilaMutation(s): 0 
EC: 3.6.4.10
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-like proteinH [auth LA]254Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3-like proteinI [auth LB]388Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-like proteinJ [auth LC]365Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l5-like proteinK [auth LD]304Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6L [auth LE]200Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l7-like proteinM [auth LF]249Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8N [auth LG]262Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l9-like proteinO [auth LH]192Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10-like proteinP [auth LI]219Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal proteinQ [auth LJ]173Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12-like proteinR [auth LK]165Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13S [auth LL]213Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-like proteinT [auth LM]142Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15U [auth LN]203Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-like proteinV [auth LO]204Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l17-like proteinW [auth LP]186Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18-like proteinX [auth LQ]213Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19Y [auth LR]192Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20Z [auth LS]174Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l21-like proteinAA [auth LT]160Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-like proteinBA [auth LU]127Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l23-like proteinCA [auth LV]139Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24DA [auth LW]161Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25-like proteinEA [auth LX]156Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-like proteinFA [auth LY]138Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27GA [auth LZ]135Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18e/L15P domain-containing proteinHA [auth La]149Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29IA [auth Lb]65Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l30-like proteinJA [auth Lc]108Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal proteinKA [auth Ld]120Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32-like proteinLA [auth Le]131Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l33-like proteinMA [auth Lf]109Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein l34-like proteinNA [auth Lg]119Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
dolichyl-diphosphooligosaccharide--protein glycotransferaseOA [auth Lh]126Thermochaetoides thermophilaMutation(s): 0 
EC: 2.4.99.18
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36PA [auth Li]110Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37QA [auth Lj]95Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38RA [auth Lk]80Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G2Q8J4 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39SA [auth Ll]51Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for Q2H9R2 (Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like domain-containing proteinTA [auth Lm]128Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for A0A2A9PNA8 (Ophiocordyceps unilateralis)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-AUA [auth Ln],
YA [auth Lr]		25Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L44-like proteinVA [auth Lo]106Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SBZ6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-like proteinWA [auth Lp]92Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal proteinXA [auth Lq]147Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0ZA [auth Ls]312Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0AB [auth SA]285Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1BB [auth SB]255Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2-like proteinCB [auth SC]263Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3-like proteinDB [auth SD]254Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4EB [auth SE]264Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s5-like proteinFB [auth SF]212Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6GB [auth SG]239Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7HB [auth SH]203Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8IB [auth SI]202Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s9-like proteinJB [auth SJ]190Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s10-like proteinKB [auth SK]159Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-like proteinLB [auth SL]161Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SF00 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12MB [auth SM]144Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13-like proteinNB [auth SN]151Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-like proteinOB [auth SO]150Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SFL1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s15-like proteinPB [auth SP]153Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S084 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-like proteinQB [auth SQ]143Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SBR7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-like proteinRB [auth SR]143Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S871 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal proteinSB [auth SS]156Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-like proteinTB [auth ST]153Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SFK8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20-like proteinUB [auth SU]116Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S379 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-like proteinVB [auth SV]98Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SI21 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-like proteinWB [auth SW]130Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s23-like proteinXB [auth SX]145Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RY17 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24YB [auth SY]136Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for P0CU28 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25ZB [auth SZ]99Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S1Y9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26AC [auth Sa]119Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein s27-like proteinBC [auth Sb]82Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-like proteinCC [auth Sc]68Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29DC [auth Sd]56Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for Q2HB68 (Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970))
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30EC [auth Se]61Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for Q2H4C5 (Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970))
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27a-like proteinFC [auth Sf]154Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase 2GC [auth D]371Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0063100
UniProt
Find proteins for G0SEA9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 1
MoleculeChains LengthOrganismImage
28S rRNAA [auth 1]3,337Thermochaetoides thermophila
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Entity ID: 2
MoleculeChains LengthOrganismImage
18S rRNAB [auth 2]1,796Thermochaetoides thermophila DSM 1495
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth 3]120Thermochaetoides thermophila DSM 1495
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Entity ID: 4
MoleculeChains LengthOrganismImage
5.8S rRNAD [auth 4]156Thermochaetoides thermophila DSM 1495
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19_4092

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySI 586-6

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release