9PRA | pdb_00009pra

In Situ Structure of the Human Mitoribosome Large Subunit 39S in Complex with EF-Tu

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2025-07-23 Released: 2026-02-18 
  • Deposition Author(s): Wang, S., Xiong, Y., Zhang, Y.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 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

Structural basis of TACO1-mediated efficient mitochondrial translation.

Wang, S.Brischigliaro, M.Zhang, Y.Wu, C.Zheng, W.Barrientos, A.Xiong, Y.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-69156-y
  • Primary Citation of Related Structures:  
    9OLF, 9PR4, 9PRA, 9PRD, 9PRQ, 9PRX, 9PS0, 9PS7, 9PSI, 9PSM

  • PubMed Abstract: 

    Translation elongation is a universally conserved step in protein synthesis, relying on elongation factors that engage the ribosomal L7/L12 stalk to mediate aminoacyl-tRNA delivery, accommodation, and ribosomal translocation. Using in organello cryo-electron microscopy, we reveal how the mitochondrial translation accelerator TACO1 promotes efficient elongation on human mitoribosomes. TACO1 binds the mitoribosomal region typically bound by elongation factor Tu (mtEF-Tu), bridging the large and small subunits via contacts with 16S rRNA, bL12m, A-site tRNA, and uS12m. While active throughout elongation, TACO1 is especially critical when translating polyproline motifs. Its absence prolongs mtEF-Tu residence in A/T states, causes persistent mitoribosomal stalling and premature subunit dissociation. Structural analyses indicate that TACO1 competes with mtEF-Tu for mitoribosome binding, stabilizes A-site tRNA, and enhances peptidyl transfer through a mechanism distinct from EF-P and eIF5A. These findings suggest that bacterial TACO1 orthologs may serve analogous roles, highlighting an evolutionarily conserved strategy for maintaining elongation efficiency during challenging translation events.


  • Organizational Affiliation
    • Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialA [auth 0]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106591 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialB [auth 1]65Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243147 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrialC [auth 2]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130312 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialD [auth 3]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132313 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrialE [auth 4]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171421 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrialF [auth 5]423Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116221 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrialG [auth 6]380Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204316 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrialH [auth 7]338Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000154719 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrialI [auth 8]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185608 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L41, mitochondrialJ [auth 9]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182154 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L45, mitochondrialK [auth d]306Homo sapiensMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondrialL [auth e]279Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000259494 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialM [auth f]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175581 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialN [auth D]305Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112651 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialO [auth E]348Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114686 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialP [auth F]311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105364 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L12, mitochondrial198Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000262814 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialR [auth H]267Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143436 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialS [auth I]261Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159111 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialT [auth J]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174547 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13mU [auth K]178Homo sapiensMutation(s): 1 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialV [auth L]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000180992 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialW [auth M]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137547 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialX [auth N]251Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166902 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialY [auth O]175Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000158042 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L18, mitochondrialZ [auth P]180Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112110 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialAA [auth Q]292Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115364 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L20, mitochondrialBA [auth R]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242485 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L21, mitochondrialCA [auth S]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197345 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L22, mitochondrialDA [auth T]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000082515 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L23, mitochondrialEA [auth U]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000214026 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrialFA [auth V]216Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143314 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L27, mitochondrialGA [auth W]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108826 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L28, mitochondrialHA [auth X]256Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086504 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L47, mitochondrialIA [auth Y]250Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136522 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L30, mitochondrialJA [auth Z]161Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185414 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L43, mitochondrialKA [auth b]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000055950 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrialLA [auth g]166Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149792 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L50, mitochondrialMA [auth h]158Homo sapiensMutation(s): 0 
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PHAROS:  Q8N5N7
GTEx:  ENSG00000136897 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L51, mitochondrialNA [auth i]128Homo sapiensMutation(s): 0 
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PHAROS:  Q4U2R6
GTEx:  ENSG00000111639 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L52, mitochondrialOA [auth j]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172590 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL53PA [auth k]112Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000204822 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L54, mitochondrialQA [auth l]138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183617 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrialRA [auth m]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162910 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent polypeptideSA [auth n]43Homo sapiensMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein 63, mitochondrialTA [auth o]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173141 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1UA [auth q]222Homo sapiensMutation(s): 0 
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Find proteins for Q8TAE8 (Homo sapiens)
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PHAROS:  Q8TAE8
GTEx:  ENSG00000179271 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S18a, mitochondrialVA [auth r]196Homo sapiensMutation(s): 0 
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Find proteins for Q9NVS2 (Homo sapiens)
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GTEx:  ENSG00000096080 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL1mCB [auth z]325Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000169288 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor Tu, mitochondrialDB [auth Ag]455Homo sapiensMutation(s): 0 
EC: 3.6.5.3
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Find proteins for P49411 (Homo sapiens)
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GTEx:  ENSG00000178952 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrialFB [auth c]332Homo sapiensMutation(s): 0 
EC: 3.1.26
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Find proteins for Q9H9J2 (Homo sapiens)
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GTEx:  ENSG00000135900 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialGB [auth p]206Homo sapiensMutation(s): 0 
EC: 3.1.1.29
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GTEx:  ENSG00000167862 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialHB [auth s]439Homo sapiensMutation(s): 0 
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Find proteins for Q9NP92 (Homo sapiens)
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GTEx:  ENSG00000112996 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial inner membrane protein OXA1LIB [auth OX]435Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000155463 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L42, mitochondrialJB [auth a]142Homo sapiensMutation(s): 0 
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Find proteins for Q9Y6G3 (Homo sapiens)
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GTEx:  ENSG00000198015 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial assembly of ribosomal large subunit protein 1KB [auth Ad]234Homo sapiensMutation(s): 0 
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Find proteins for Q96EH3 (Homo sapiens)
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GTEx:  ENSG00000156928 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosome and complex I assembly factor AltMIEF1LB [auth Ae]70Homo sapiensMutation(s): 0 
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Find proteins for L0R8F8 (Homo sapiens)
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialMB [auth Af]156Homo sapiensMutation(s): 0 
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Find proteins for O14561 (Homo sapiens)
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GTEx:  ENSG00000004779 
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Entity ID: 51
MoleculeChains LengthOrganismImage
16S mitochondrial rRNAEB [auth A]1,558Homo sapiens
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Entity ID: 60
MoleculeChains LengthOrganismImage
mitochondrial tRNAValNB [auth B]72Homo sapiens
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FES (Subject of Investigation/LOI)
Query on FES

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CC [auth r]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
SPD (Subject of Investigation/LOI)
Query on SPD

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EC [auth A],
FC [auth A]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
VAL
Query on VAL

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PI [auth B]VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
PUT
Query on PUT

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GC [auth A]1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN
Query on ZN

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OB [auth 0],
QB [auth 4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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AI [auth A]
BC [auth o]
BI [auth A]
CI [auth A]
DC [auth A]
AI [auth A],
BC [auth o],
BI [auth A],
CI [auth A],
DC [auth A],
DI [auth A],
EI [auth A],
FI [auth A],
GI [auth A],
HI [auth A],
II [auth A],
JI [auth A],
KI [auth A],
LI [auth A],
MI [auth A],
NH [auth A],
NI [auth A],
OH [auth A],
OI [auth A],
PB [auth 3],
PH [auth A],
QH [auth A],
RB [auth 6],
RH [auth A],
SH [auth A],
TH [auth A],
UB [auth D],
UH [auth A],
VH [auth A],
WH [auth A],
XB [auth M],
XH [auth A],
YB [auth N],
YH [auth A],
ZB [auth W],
ZH [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth g]
AD [auth A]
AE [auth A]
AF [auth A]
AG [auth A]
AC [auth g],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
AH [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
BH [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
CH [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
DH [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth A],
EH [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
FH [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
GH [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
HH [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
IH [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
JH [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
KH [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
LH [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
MH [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth A],
SB [auth D],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth A],
TB [auth D],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth A],
VB [auth E],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth A],
WB [auth I],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
4HH
Query on 4HH
MB [auth Af]L-PEPTIDE LINKINGC14 H28 N3 O9 P SSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419:
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-18
    Type: Initial release