7OI9

Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 3B


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

A distinct assembly pathway of the human 39S late pre-mitoribosome.

Cheng, J.Berninghausen, O.Beckmann, R.

(2021) Nat Commun 12: 4544-4544

  • DOI: https://doi.org/10.1038/s41467-021-24818-x
  • Primary Citation of Related Structures:  
    7OI6, 7OI7, 7OI8, 7OI9, 7OIA, 7OIB, 7OIC, 7OID, 7OIE

  • PubMed Abstract: 

    Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states. Besides the MALSU1 complex used as bait for affinity purification, we identify several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involve rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we find deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome.


  • Organizational Affiliation

    Gene Center and Department for Biochemistry, LMU Munich, München, Germany. jcheng@genzentrum.lmu.de.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialA [auth D]305Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112651 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialB [auth E]348Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114686 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialC [auth F]311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105364 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialD [auth H]267Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143436 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialE [auth I]261Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159111 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialF [auth J]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174547 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialG [auth K]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172172 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialH [auth L]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000180992 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialI [auth M]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137547 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialJ [auth N]251Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166902 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialK [auth O]175Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000158042 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L18, mitochondrialL [auth P]180Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112110 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialM [auth Q]292Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115364 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L20, mitochondrialN [auth R]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242485 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L21, mitochondrialO [auth S]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197345 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L22, mitochondrialP [auth T]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000082515 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L23, mitochondrialQ [auth U]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000214026 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrialR [auth V]216Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143314 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L27, mitochondrialS [auth W]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108826 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L28, mitochondrialT [auth X]256Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086504 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L47, mitochondrialU [auth Y]250Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136522 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L30, mitochondrialV [auth Z]161Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185414 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialW [auth 0]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106591 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialX [auth 1]65Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243147 
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MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrialY [auth 2]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130312 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialZ [auth 3]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132313 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrialAA [auth 5]423Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116221 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrialBA [auth 6]380Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204316 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrialCA [auth 7]338Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000154719 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrialDA [auth 8]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185608 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L41, mitochondrialEA [auth 9]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182154 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L42, mitochondrialFA [auth a]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198015 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L43, mitochondrialGA [auth b]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000055950 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrialHA [auth c]332Homo sapiensMutation(s): 0 
EC: 3.1.26
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GTEx:  ENSG00000135900 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L45, mitochondrialIA [auth d]306Homo sapiensMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondrialJA [auth e]279Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000259494 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialKA [auth f]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175581 
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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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GTEx:  ENSG00000136897 
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UniProt GroupQ8N5N7
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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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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
39S ribosomal protein L53, mitochondrialPA [auth k]112Homo sapiensMutation(s): 0 
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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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Find proteins for Q7Z7F7 (Homo sapiens)
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GTEx:  ENSG00000162910 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein 63, mitochondrialSA [auth o]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173141 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialTA [auth p]206Homo sapiensMutation(s): 0 
EC: 3.1.1.29
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GTEx:  ENSG00000167862 
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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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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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GTEx:  ENSG00000096080 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialWA [auth s]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112996 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial assembly of ribosomal large subunit protein 1XA [auth u]234Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156928 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
MIEF1 upstream open reading frame proteinYA [auth v]70Homo sapiensMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialZA [auth w]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000004779 
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Entity ID: 53
MoleculeChains LengthOrganismImage
16S rRNAAB [auth A]1,559Homo sapiens
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Entity ID: 54
MoleculeChains LengthOrganismImage
mitochondrial Val tRNABB [auth B]69Homo 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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GB [auth v]4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
ZN
Query on ZN

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DB [auth 0],
FB [auth r]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth A]
AD [auth A]
BC [auth A]
BD [auth A]
CB [auth W]
AC [auth A],
AD [auth A],
BC [auth A],
BD [auth A],
CB [auth W],
CC [auth A],
DC [auth A],
EB [auth g],
EC [auth A],
FC [auth A],
GC [auth A],
HB [auth A],
HC [auth A],
IB [auth A],
IC [auth A],
JB [auth A],
JC [auth A],
KB [auth A],
KC [auth A],
LB [auth A],
LC [auth A],
MB [auth A],
MC [auth A],
NB [auth A],
NC [auth A],
OB [auth A],
OC [auth A],
PB [auth A],
PC [auth A],
QB [auth A],
QC [auth A],
RB [auth A],
RC [auth A],
SB [auth A],
SC [auth A],
TB [auth A],
TC [auth A],
UB [auth A],
UC [auth A],
VB [auth A],
VC [auth A],
WB [auth A],
WC [auth A],
XB [auth A],
XC [auth A],
YB [auth A],
YC [auth A],
ZB [auth A],
ZC [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Data collection
  • Version 1.2: 2024-07-10
    Changes: Data collection