6Z1P

Structure of the mitochondrial ribosome from Tetrahymena thermophila


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation.

Tobiasson, V.Amunts, A.

(2020) Elife 9

  • DOI: 10.7554/eLife.59264
  • Primary Citation of Related Structures:  
    6Z1P

  • PubMed Abstract: 
  • To understand the steps involved in the evolution of translation, we used Tetrahymena thermophila , a ciliate with high coding capacity of the mitochondrial genome, as the model organism and characterized its mitochondrial ribosome (mitoribosome) using cryo-EM ...

    To understand the steps involved in the evolution of translation, we used Tetrahymena thermophila , a ciliate with high coding capacity of the mitochondrial genome, as the model organism and characterized its mitochondrial ribosome (mitoribosome) using cryo-EM. The structure of the mitoribosome reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit, while the large subunit lacks 5S rRNA. The structure also shows that the small subunit head is constrained, tRNA binding sites are formed by mitochondria-specific protein elements, conserved protein bS1 is excluded, and bacterial RNA polymerase binding site is blocked. We provide evidence for anintrinsic protein targeting system through visualization of mitochondria-specific mL105 by the exit tunnel that would facilitate the recruitment of a nascent polypeptide. Functional protein uS3m is encoded by three complementary genes from the nucleus and mitochondrion, establishing a link between genetic drift and mitochondrial translation. Finally, we reannotated nine open reading frames in the mitochondrial genome that code for mitoribosomal proteins.


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L2C [auth Ac]262Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth Ad]439Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00637400
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Find proteins for Q22HG3 (Tetrahymena thermophila (strain SB210))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth Ae]358Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00564280
UniProt
Find proteins for I7MGP2 (Tetrahymena thermophila (strain SB210))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Ymf69F [auth Af]68Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ymf60G [auth Ag]179Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
bL7/L12mH [auth Ah]106Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
bL7/12mI [auth Ai]61Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
bL7/12mJ [auth Aj]69Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L7/L12 carboxy-terminal domain proteinK [auth Ak]105Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00918510
UniProt
Find proteins for Q24IM4 (Tetrahymena thermophila (strain SB210))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L9, amine-terminal domain proteinL [auth Al]223Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00697430
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Ymf74M [auth Am]166Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L11, amine-terminal domain proteinN [auth An]158Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_000585349
UniProt
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13O [auth Ao]391Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_001207659
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L14P [auth Ap]119Tetrahymena thermophila SB210Mutation(s): 0 
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Find proteins for Q950Y1 (Tetrahymena thermophila)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L15, putativeQ [auth Aq]305Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00136240
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Find proteins for I7MF78 (Tetrahymena thermophila (strain SB210))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L16R [auth Ar]143Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17S [auth As]237Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00106969
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Find proteins for A4VE95 (Tetrahymena thermophila (strain SB210))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
bL19mT [auth At]242Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00408950
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20U [auth Au]170Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_01034460
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Find proteins for Q235I3 (Tetrahymena thermophila (strain SB210))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21V [auth Av]235Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00280990
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Find proteins for I7LVD3 (Tetrahymena thermophila (strain SB210))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L22/L17eW [auth Aw]364Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00052510
UniProt
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L23, putativeX [auth Ax]138Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00822340
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24Y [auth Ay]234Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00697420
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
bL25mZ [auth Az]321Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00220590
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27AA237Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00419850
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Find proteins for I7M068 (Tetrahymena thermophila (strain SB210))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L28BA [auth AB]289Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00140980
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Find proteins for I7LU83 (Tetrahymena thermophila (strain SB210))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
39-S ribosomal protein L47CA [auth AC]307Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00160960
UniProt
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
bL32mDA [auth AD]36Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33EA [auth AE]64Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_01013180
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
bL35mFA [auth AF]164Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00189300
UniProt
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal proteinGA [auth AG]93Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_000446568
UniProt
Find proteins for W7XH61 (Tetrahymena thermophila (strain SB210))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
mL40HA [auth AH]199Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00716190
UniProt
Find proteins for I7LT48 (Tetrahymena thermophila (strain SB210))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L27IA [auth AI]155Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00316160
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L51/S25/CI-B8 domain proteinJA [auth AJ]179Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00016270
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
mL46KA [auth AK]309Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00558550
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Large subunit ribosomal proteinLA [auth AL]145Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00616380
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
mL53MA [auth AM]184Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00313610
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
mL54NA [auth AN]158Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00455100
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
mL64OA [auth AO]155Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00785870
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
mL101PA [auth AP]386Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00614680
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
mL102QA [auth AQ]109Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_000659131
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
mL103RA [auth AR]348Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00220600
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
mL104SA [auth AS]764Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00420290
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Entity ID: 46
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Signal peptide-binding domain proteinTA [auth AT]299Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_000931898
UniProt
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
mL106UA [auth AU]499Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00582070
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Iron-binding zinc finger CDGSH type proteinVA [auth AV]160Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00637600
UniProt
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
Ymf73YA [auth Bc]159Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
Ymf64ZA [auth Bd]330Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 53
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Ymf76AB [auth Be]405Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5BB [auth Bf]351Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00497450
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S6CB [auth Bg]141Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00535550
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Ymf63DB [auth Bh]276Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 57
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Ribosomal protein S9EB [auth Bi]737Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00670170
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Find proteins for I7M4A2 (Tetrahymena thermophila (strain SB210))
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Entity ID: 58
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Ymf59FB [auth Bj]152Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
Ymf61GB [auth Bk]238Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 60
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Ribosomal protein S12HB [auth Bl]133Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S13IB [auth Bm]276Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 62
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Ribosomal protein S14JB [auth Bn]101Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 63
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30S ribosomal protein S15KB [auth Bo]196Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00157810
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16LB [auth Bp]437Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00444330
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17MB [auth Bq]182Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00585250
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S18NB [auth Br]549Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00194530
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S19OB [auth Bs]98Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
bS21mPB [auth Bt]102Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_01108550
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
mS23QB [auth Bu]567Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_01207720
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
mS26RB [auth Bv]579Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00561490
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Entity ID: 71
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Ribosomal death-associated proteinSB [auth Bw]703Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00013070
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Entity ID: 72
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mS31TB [auth Bx]719Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00797930
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
mS33UB [auth By]132Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00221170
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
mS34VB [auth Bz]147Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00492510
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal subunit proteinWB [auth BA]149Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00194710
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
mS37XB [auth BB]112Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00780710
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Entity ID: 77
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mS38YB [auth BC]37Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 78
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IGR motif proteinZB [auth BD]130Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00721630
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
mS45AC [auth BE]464Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00046550
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
mS75BC [auth BF]23Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
mS76CC [auth BG]182Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_01212860
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
mS77DC [auth BH]63Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 83
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Enoyl-CoA hydratase/isomeraseEC [auth BI]1451Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00414440
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
mS78FC [auth BJ]1539Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00145010
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Entity ID: 85
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mS79GC [auth BK]267Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00047280
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Entity ID: 86
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SelR domain proteinHC [auth BL]310Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00160750
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Entity ID: 87
MoleculeChainsSequence LengthOrganismDetailsImage
mS81IC [auth BM]355Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00853090
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Entity ID: 88
MoleculeChainsSequence LengthOrganismDetailsImage
mS82JC [auth BN]283Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00703660
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Entity ID: 89
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PARP alpha-helical domain-containing protein,mS83KC [auth BO]142Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00214830
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Entity ID: 90
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mS84,mS84LC [auth BP]100Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 91
MoleculeChainsSequence LengthOrganismDetailsImage
mS85MC [auth BQ]1032Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00550810
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Entity ID: 92
MoleculeChainsSequence LengthOrganismDetailsImage
Iron donor protein CyaYNC [auth BR]143Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00989460
UniProt
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Entity ID: 93
MoleculeChainsSequence LengthOrganismDetailsImage
mS87OC [auth BS]1086Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00647339
UniProt
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Entity ID: 94
MoleculeChainsSequence LengthOrganismDetailsImage
mS88PC [auth BT]297Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 95
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mS89QC [auth BU]439Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00835120
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Entity ID: 96
MoleculeChainsSequence LengthOrganismDetailsImage
mS90RC [auth BV]310Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_01057750
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Entity ID: 97
MoleculeChainsSequence LengthOrganismDetailsImage
mS91SC [auth BW]285Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 98
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Ribosomal protein S3TC [auth BX]151Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 99
MoleculeChainsSequence LengthOrganismDetailsImage
mS93UC [auth BY]327Tetrahymena thermophila SB210Mutation(s): 0 
Gene Names: TTHERM_00522240
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Entity ID: 1
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LSU rRNA_1A [auth Aa]278Tetrahymena thermophila SB210
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