5OOL

Structure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structures of the human mitochondrial ribosome in native states of assembly.

Brown, A.Rathore, S.Kimanius, D.Aibara, S.Bai, X.C.Rorbach, J.Amunts, A.Ramakrishnan, V.

(2017) Nat Struct Mol Biol 24: 866-869

  • DOI: https://doi.org/10.1038/nsmb.3464
  • Primary Citation of Related Structures:  
    5OOL, 5OOM

  • PubMed Abstract: 

    Mammalian mitochondrial ribosomes (mitoribosomes) have less rRNA content and 36 additional proteins compared with the evolutionarily related bacterial ribosome. These differences make the assembly of mitoribosomes more complex than the assembly of bacterial ribosomes, but the molecular details of mitoribosomal biogenesis remain elusive. Here, we report the structures of two late-stage assembly intermediates of the human mitoribosomal large subunit (mt-LSU) isolated from a native pool within a human cell line and solved by cryo-EM to ∼3-Å resolution. Comparison of the structures reveals insights into the timing of rRNA folding and protein incorporation during the final steps of ribosomal maturation and the evolutionary adaptations that are required to preserve biogenesis after the structural diversification of mitoribosomes. Furthermore, the structures redefine the ribosome silencing factor (RsfS) family as multifunctional biogenesis factors and identify two new assembly factors (L0R8F8 and mt-ACP) not previously implicated in mitoribosomal biogenesis.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialC [auth D]305Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112651 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialD [auth E]348Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114686 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialE [auth F]311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105364 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialF [auth H]267Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143436 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialG [auth I]261Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159111 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialH [auth J]192Homo sapiensMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialI [auth K]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172172 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialJ [auth L]145Homo sapiensMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialK [auth M]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137547 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialL [auth N]251Homo sapiensMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialM [auth O]175Homo sapiensMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L18, mitochondrialN [auth P]180Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112110 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialO [auth Q]292Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115364 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L20, mitochondrialP [auth R]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242485 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L21, mitochondrialQ [auth S]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197345 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L22, mitochondrialR [auth T]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000082515 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L23, mitochondrialS [auth U]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000214026 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrialT [auth V]216Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143314 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L27, mitochondrialU [auth W]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108826 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L28, mitochondrialV [auth X]256Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086504 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L47, mitochondrialW [auth Y]250Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136522 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L30, mitochondrialX [auth Z]161Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185414 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialY [auth 0]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106591 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialZ [auth 1]65Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243147 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrialAA [auth 2]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130312 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialBA [auth 3]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132313 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrialCA [auth 4]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171421 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrialDA [auth 5]423Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116221 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrialEA [auth 6]380Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204316 
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MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrialFA [auth 7]338Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000154719 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrialGA [auth 8]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185608 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L41, mitochondrialHA [auth 9]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182154 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L42, mitochondrialIA [auth a]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198015 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L43, mitochondrialJA [auth b]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000055950 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrialKA [auth c]332Homo sapiensMutation(s): 0 
EC: 3.1.26
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GTEx:  ENSG00000135900 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L45, mitochondrialLA [auth d]306Homo sapiensMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondrialMA [auth e]279Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000259494 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialNA [auth f]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175581 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrialOA [auth g]166Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149792 
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UniProt GroupQ13405
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L50, mitochondrialPA [auth h]158Homo sapiensMutation(s): 0 
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PHAROS:  Q8N5N7
GTEx:  ENSG00000136897 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L51, mitochondrialQA [auth i]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111639 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L52, mitochondrialRA [auth j]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172590 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L53, mitochondrialSA [auth k]112Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204822 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L54, mitochondrialTA [auth l]138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183617 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrialUA [auth m]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162910 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein 63, mitochondrialVA [auth o]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173141 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialWA [auth p]206Homo sapiensMutation(s): 0 
EC: 3.1.1.29
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GTEx:  ENSG00000167862 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1XA [auth q]222Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000179271 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S18a, mitochondrialYA [auth r]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096080 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialZA [auth s]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112996 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein or protein extensionAB [auth t]28Homo sapiensMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial assembly of ribosomal large subunit protein 1BB [auth u]234Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156928 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
MIEF1 upstream open reading frame proteinCB [auth v]70Homo sapiensMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialDB [auth w]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000004779 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNA1,559Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
mitochondrial tRNAVal69Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PNS
Query on PNS

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VE [auth v]4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
ZN
Query on ZN

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OE [auth I],
SE [auth 0],
TE [auth 4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth A]
AD [auth A]
AE [auth A]
BC [auth A]
BD [auth A]
AC [auth A],
AD [auth A],
AE [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth D],
OB [auth A],
OC [auth A],
OD [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth M],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth T],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth W],
SB [auth A],
SC [auth A],
SD [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth g],
VB [auth A],
VC [auth A],
VD [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.11.1
RECONSTRUCTIONRELION2.0.1

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references
  • Version 1.2: 2017-10-18
    Changes: Database references
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-12-11
    Changes: Other
  • Version 1.5: 2023-03-15
    Changes: Advisory, Database references, Derived calculations, Refinement description