8APN

Structure of the mitochondrial ribosome from Polytomella magna with tRNA bound to the P site


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 1.2 of the entry. See complete history


Literature

Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.

Tobiasson, V.Berzina, I.Amunts, A.

(2022) Nat Commun 13: 6132-6132

  • DOI: https://doi.org/10.1038/s41467-022-33582-5
  • Primary Citation of Related Structures:  
    8A22, 8APN, 8APO

  • PubMed Abstract: 

    Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature. Here, we report a 2.9 Å resolution structure of the mitoribosome from the alga Polytomella magna harbouring a reduced rRNA split into 13 fragments. We found that the rRNA contains a non-canonical reduced form of the 5S, as well as a permutation of the LSU domain I. The mt-5S rRNA is stabilised by mL40 that is also found in mitoribosomes lacking the 5S, which suggests an evolutionary pathway. Through comparison to other ribosomes with fragmented rRNAs, we observe that the pattern is shared across large evolutionary distances, and between cellular compartments, indicating an evolutionary convergence and supporting the concept of a primordial fragmented ribosome. On the protein level, eleven peripherally associated HEAT-repeat proteins are involved in the binding of 3' rRNA termini, and the structure features a prominent pseudo-trimer of one of them (mL116). Finally, in the exit tunnel, mL128 constricts the tunnel width of the vestibular area, and mL105, a homolog of a membrane targeting component mediates contacts with an inner membrane bound insertase. Together, the structural analysis provides insight into the evolution of the ribosomal machinery in mitochondria.


  • Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden.


Macromolecules

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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uL2mJ [auth Aa]306Polytomella magnaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
uL3mK [auth Ab]306Polytomella magnaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
uL4mL [auth Ac]303Polytomella magnaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
uL5mM [auth Ad]193Polytomella magnaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL6mN [auth Ae]242Polytomella magnaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uL9mO [auth Af]56Polytomella magnaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
uL13mP [auth Ah]186Polytomella magnaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical proteinQ [auth Ai]121Polytomella magnaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
uL15mR [auth Aj]206Polytomella magnaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
uL16mS [auth Ak]166Polytomella magnaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
bL17mT [auth Al]173Polytomella magnaMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
uL18mU [auth Am]114Polytomella magnaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
bL19mV [auth An]170Polytomella magnaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
bL20mW [auth Ao]117Polytomella magnaMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
bL21mX [auth Ap]200Polytomella magnaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
uL22mY [auth Aq]188Polytomella magnaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
uL23mZ [auth Ar]155Polytomella magnaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
bL24mAA [auth As]115Polytomella magnaMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
bL25mBA [auth At]253Polytomella magnaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
bL27mCA [auth Au]142Polytomella magnaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
bL28mDA [auth Av]129Polytomella magnaMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
uL29mEA [auth Aw]123Polytomella magnaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
uL30mFA [auth Ax]176Polytomella magnaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
bL31mGA [auth Ay]72Polytomella magnaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
bL32mHA [auth Az]59Polytomella magnaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
bL33mIA [auth AA]50Polytomella magnaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
bL34mJA [auth AB]50Polytomella magnaMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
bL35mKA [auth AC]139Polytomella magnaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
bL36mLA [auth AD]47Polytomella magnaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
mL40MA [auth AE]92Polytomella magnaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
mL41NA [auth AF]93Polytomella magnaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
mL43OA [auth AG]121Polytomella magnaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
mL46PA [auth AH]176Polytomella magnaMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
mL63QA [auth AI]64Polytomella magnaMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
mL64RA [auth AJ]122Polytomella magnaMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
mL87SA [auth AK]139Polytomella magnaMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
mL116TA [auth AL]394Polytomella magnaMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
mL116UA [auth AM]419Polytomella magnaMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
mL116VA [auth AN]420Polytomella magnaMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
mL118WA [auth AO]377Polytomella magnaMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
mL120XA [auth Xa]199Polytomella magnaMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
mL121YA [auth Xb]244Polytomella magnaMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
mL122ZA [auth Xc]57Polytomella magnaMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
mL123AB [auth Xd]413Polytomella magnaMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
mL124BB [auth Xe]483Polytomella magnaMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
mL125CB [auth Xf]201Polytomella magnaMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
mL126DB [auth Xg]410Polytomella magnaMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
mL127EB [auth Xh]143Polytomella magnaMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
mL128FB [auth Xi]24Polytomella magnaMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
mL129GB [auth Xj]71Polytomella magnaMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
bS1mLB [auth Ba]242Polytomella magnaMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
uS2mMB [auth Bb]236Polytomella magnaMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
uS3mNB [auth Bc]289Polytomella magnaMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
uS4mOB [auth Bd]221Polytomella magnaMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
uS5mPB [auth Be]228Polytomella magnaMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
uS6mQB [auth Bf]119Polytomella magnaMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
uS7mRB [auth Bg]112Polytomella magnaMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
uS8mSB [auth Bh]374Polytomella magnaMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
uS9mTB [auth Bi]282Polytomella magnaMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
uS10mUB [auth Bj]401Polytomella magnaMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
uS11mVB [auth Bk]116Polytomella magnaMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
uS12mWB [auth Bl]123Polytomella magnaMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
uS13mXB [auth Bm]113Polytomella magnaMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
uS14mYB [auth Bn]118Polytomella magnaMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
uS15mZB [auth Bo]167Polytomella magnaMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
bS16mAC [auth Bp]123Polytomella magnaMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
uS17mBC [auth Bq]130Polytomella magnaMutation(s): 0 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
bS18mCC [auth Br]90Polytomella magnaMutation(s): 0 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
bS19mDC [auth Bs]92Polytomella magnaMutation(s): 0 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
bS21mEC [auth Bt]75Polytomella magnaMutation(s): 0 
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
mS23FC [auth Bu]167Polytomella magnaMutation(s): 0 
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
mS26GC [auth Bv]164Polytomella magnaMutation(s): 0 
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
mS29HC [auth Bw]349Polytomella magnaMutation(s): 0 
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
mS31IC [auth Bx]621Polytomella magnaMutation(s): 0 
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Entity ID: 88
MoleculeChains Sequence LengthOrganismDetailsImage
mS33JC [auth By]80Polytomella magnaMutation(s): 0 
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Entity ID: 89
MoleculeChains Sequence LengthOrganismDetailsImage
mS34KC [auth Bz]119Polytomella magnaMutation(s): 0 
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Entity ID: 90
MoleculeChains Sequence LengthOrganismDetailsImage
mS35LC [auth BA]176Polytomella magnaMutation(s): 0 
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Entity ID: 91
MoleculeChains Sequence LengthOrganismDetailsImage
mS37MC [auth BB]84Polytomella magnaMutation(s): 0 
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Entity ID: 92
MoleculeChains Sequence LengthOrganismDetailsImage
mS45NC [auth BC]270Polytomella magnaMutation(s): 0 
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Entity ID: 93
MoleculeChains Sequence LengthOrganismDetailsImage
mS38OC [auth BD]31Polytomella magnaMutation(s): 0 
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Entity ID: 94
MoleculeChains Sequence LengthOrganismDetailsImage
mS106PC [auth BE]171Polytomella magnaMutation(s): 0 
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Entity ID: 95
MoleculeChains Sequence LengthOrganismDetailsImage
mS107QC [auth BF]370Polytomella magnaMutation(s): 0 
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Entity ID: 96
MoleculeChains Sequence LengthOrganismDetailsImage
uS4m-2RC [auth Ya]180Polytomella magnaMutation(s): 0 
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Entity ID: 97
MoleculeChains Sequence LengthOrganismDetailsImage
mS108SC [auth Yb]50Polytomella magnaM