6XYW

Structure of the plant mitochondrial ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.86 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

Cryo-EM structure of the RNA-rich plant mitochondrial ribosome.

Waltz, F.Soufari, H.Bochler, A.Giege, P.Hashem, Y.

(2020) Nat Plants 6: 377-383

  • DOI: https://doi.org/10.1038/s41477-020-0631-5
  • Primary Citation of Related Structures:  
    6XYW

  • PubMed Abstract: 

    The vast majority of eukaryotic cells contain mitochondria, essential powerhouses and metabolic hubs 1 . These organelles have a bacterial origin and were acquired during an early endosymbiosis event 2 . Mitochondria possess specialized gene expression systems composed of various molecular machines, including the mitochondrial ribosomes (mitoribosomes). Mitoribosomes are in charge of translating the few essential mRNAs still encoded by mitochondrial genomes 3 . While chloroplast ribosomes strongly resemble those of bacteria 4,5 , mitoribosomes have diverged significantly during evolution and present strikingly different structures across eukaryotic species 6-10 . In contrast to animals and trypanosomatids, plant mitoribosomes have unusually expanded ribosomal RNAs and have conserved the short 5S rRNA, which is usually missing in mitoribosomes 11 . We have previously characterized the composition of the plant mitoribosome 6 , revealing a dozen plant-specific proteins in addition to the common conserved mitoribosomal proteins. In spite of the tremendous recent advances in the field, plant mitoribosomes remained elusive to high-resolution structural investigations and the plant-specific ribosomal features of unknown structures. Here, we present a cryo-electron microscopy study of the plant 78S mitoribosome from cauliflower at near-atomic resolution. We show that most of the plant-specific ribosomal proteins are pentatricopeptide repeat proteins (PPRs) that deeply interact with the plant-specific rRNA expansion segments. These additional rRNA segments and proteins reshape the overall structure of the plant mitochondrial ribosome, and we discuss their involvement in the membrane association and mRNA recruitment prior to translation initiation. Finally, our structure unveils an rRNA-constructive phase of mitoribosome evolution across eukaryotes.


  • Organizational Affiliation

    Institut Européen de Chimie et Biologie, U1212 Inserm, Université de Bordeaux, Pessac, France.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2, mitochondrialA [auth Aa]349Arabidopsis thalianaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Expressed proteinB [auth Ab]214Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3-2, mitochondrialC [auth Ac]324Arabidopsis thalianaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L35D [auth AD]173Arabidopsis thalianaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth Ad]300Arabidopsis thalianaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5, mitochondrialF [auth Ae]185Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L6G [auth Af]102Arabidopsis thalianaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L9/RNase H1H [auth Ag]221Arabidopsis thalianaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
At4g35490I [auth Ai]155Arabidopsis thalianaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
At1g01640J [auth Aj]205Arabidopsis thalianaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein HLP, mitochondrialK [auth Ak]173Arabidopsis thalianaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18e/L15 superfamily proteinL [auth Al]281Arabidopsis thalianaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16, mitochondrialM [auth Am]179Arabidopsis thalianaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
At5g09770N [auth An]160Arabidopsis thalianaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
At5g27820O [auth Ao]114Arabidopsis thalianaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
At1g24240/F3I6_17P [auth Ap]222Arabidopsis thalianaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20Q [auth Aq]126Arabidopsis thalianaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21, mitochondrialR [auth Ar]270Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q8L9A0 (Arabidopsis thaliana)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
AT1G52370 proteinS [auth As]269Arabidopsis thalianaMutation(s): 0 
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Find proteins for Q56W16 (Arabidopsis thaliana)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
At4g39880T [auth At]178Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24U [auth Au]159Arabidopsis thalianaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain-containing proteinV [auth Av]249Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9FKZ4 (Arabidopsis thaliana)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27W [auth Aw]154Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
AT4g31460/F3L17_30X [auth Ax]212Arabidopsis thalianaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
At1g07830/F24B9_7Y [auth Ay]144Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L31Z [auth AA]76Arabidopsis thalianaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
At1g26740/T24P13_11AA [auth AB]134Arabidopsis thalianaMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
At3g06320BA [auth AC]58Arabidopsis thalianaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal proteinCA [auth AE]103Arabidopsis thalianaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
At4g05400DA [auth AF]250Arabidopsis thalianaMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
At5g40080EA [auth AG]94Arabidopsis thalianaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L51/S25/CI-B8 family proteinFA [auth AH]146Arabidopsis thalianaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
At1g14620/T5E21_15GA [auth AI]233Arabidopsis thalianaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal proteinHA [auth AJ]127Arabidopsis thalianaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
At4g22000IA [auth AK]130Arabidopsis thalianaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein At1g27435/F17L21.30JA [auth AL]81Arabidopsis thalianaMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
At1g73940/F2P9_19KA [auth AM]151Arabidopsis thalianaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
At3g51010LA [auth AN]188Arabidopsis thalianaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat-containing protein At1g60770MA [auth AO]491Arabidopsis thalianaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
rPPR*NA [auth AP]669Arabidopsis thalianaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat-containing protein PNM1, mitochondrialOA [auth AQ]521Arabidopsis thalianaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-6PA [auth AR]29Arabidopsis thalianaMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S3, mitochondrialSA [auth Bb]556Arabidopsis thalianaMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S7, mitochondrialTA [auth Bf]148Arabidopsis thalianaMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9, mitochondrialUA [auth Bh]430Arabidopsis thalianaMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10, mitochondrialVA [auth Bi]241Arabidopsis thalianaMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein S13, mitochondrialWA [auth Bl]154Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
At2g34520XA [auth Bm]164Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19, mitochondrialYA [auth Br]212Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial 28S ribosomal protein S29-like proteinZA [auth Bw]480Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S27AB [auth Bx]102Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
AT3G18240 proteinBB [auth Bz]419Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
CX9C domain-containing proteinCB [auth BA]91Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S31, mitochondrialDB [auth Bt]98Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat-containing protein At3g02650, mitochondrialEB [auth BG]576Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-5FB [auth BP]91Arabidopsis thalianaMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
mS31/mS46GB [auth BF]123Arabidopsis thalianaMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S2, mitochondrialHB [auth Ba]219Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S4, mitochondrialIB [auth Bc]362Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
At1g64880JB [auth Bd]515Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Translation elongation factor EF1B/ribosomal protein S6 family proteinKB [auth Be]139Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15a-5LB [auth Bg]129Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ribosomal protein S11, mitochondrialMB [auth Bj]314Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
At1g15810/F7H2_23NB [auth Bn]419Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16-2, chloroplastic/mitochondrialOB [auth Bo]135Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleic acid-binding, OB-fold-like proteinPB [auth Bp]116Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
F10K1.8 proteinQB [auth Bq]261Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S21 family proteinRB [auth Bs]101Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinSB [auth Bu]195Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
AT5g49210/K21P3_8TB [auth Bv]195Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal S34 proteinUB [auth By]142Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
mS38VB [auth BB]137Arabidopsis thalianaMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
At5g26800WB [auth BC]112Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Gb|AAC32909.1XB [auth BD]420Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
3-hydroxyisobutyryl-CoA hydrolase-like protein 2, mitochondrialYB [auth BE]409Arabidopsis thalianaMutation(s): 0 
EC: 3.1.2
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
rPPR*ZB [auth BI]266Arabidopsis thalianaMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
rPPR*AC [auth BJ]349Arabidopsis thalianaMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
Adenylyl cyclaseBC [auth BH]390Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-3CC [auth BN]69Arabidopsis thalianaMutation(s): 0 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-2DC [auth BM]79Arabidopsis thalianaMutation(s): 0 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-4EC [auth BO]30Arabidopsis thalianaMutation(s): 0 
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-1FC [auth BL]64Arabidopsis thalianaMutation(s): 0 
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
At5g55140HC [auth Az]109Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10IC [auth Ah]171Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 88
MoleculeChains Sequence LengthOrganismDetailsImage
rPPR*JC [auth BK]316Arabidopsis thalianaMutation(s): 0 
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Entity ID: 89
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S12, mitochondrialKC [auth Bk]125Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains LengthOrganismImage
RNA (2842-MER)QA [auth 1]2,842Arabidopsis thaliana
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Entity ID: 44
MoleculeChains LengthOrganismImage
RNA (118-MER)RA [auth 3]118Arabidopsis thaliana
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Entity ID: 85
MoleculeChains LengthOrganismImage
RNA (1743-MER)GC [auth 2]1,743Arabidopsis thaliana
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0.7

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceMITRA, ANR-16-CE11-0024-02

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references
  • Version 1.2: 2020-04-29
    Changes: Database references