7ODS

State B of the human mitoribosomal large subunit assembly intermediate

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

Stepwise maturation of the peptidyl transferase region of human mitoribosomes.

Lenarcic, T., Jaskolowski, M., Leibundgut, M., Scaiola, A., Schonhut, T., Saurer, M., Lee, R.G., Rackham, O., Filipovska, A., Ban, N.

(2021) Nat Commun 12: 3671-3671

  • DOI: https://doi.org/10.1038/s41467-021-23811-8
  • Primary Citation of Related Structures:  
    7ODR, 7ODS, 7ODT

  • PubMed Abstract: 

    • Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs ...

    Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. The structural basis of the mammalian mitochondrial ribosome assembly is currently not well understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving seven assembly factors. We discover that the NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by the MRM2 methyltransferase and quality control interactions with the conserved mitochondrial GTPase MTG2 that contacts the sarcin-ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit.

    Organizational Affiliation: 

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland. ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial assembly of ribosomal large subunit protein 1A [auth u]234Homo sapiensMutation(s): 0 
Gene Names: MALSU1, C7orf30
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MIEF1 upstream open reading frame proteinB [auth v]70Homo sapiensMutation(s): 0 
Gene Names: MIEF1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialC [auth w]156Homo sapiensMutation(s): 0 
Gene Names: NDUFAB1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
5-methylcytosine rRNA methyltransferase NSUN4D [auth x]384Homo sapiensMutation(s): 0 
Gene Names: NSUN4
EC: 2.1.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription termination factor 4, mitochondrialE [auth y]381Homo sapiensMutation(s): 0 
Gene Names: MTERF4, MTERFD2, HSPC096
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
rRNA methyltransferase 2, mitochondrialF [auth z]246Homo sapiensMutation(s): 0 
Gene Names: MRM2, FJH1, FTSJ2
EC: 2.1.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialG [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32, HSPC283
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Entity ID: 8
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39S ribosomal protein L33, mitochondrialH [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33, C2orf1
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Entity ID: 9
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39S ribosomal protein L34, mitochondrialI [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 10
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39S ribosomal protein L35, mitochondrialJ [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35, BM-007
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Entity ID: 11
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39S ribosomal protein L36, mitochondrialK [auth 4]103Homo sapiensMutation(s): 0 
Gene Names: MRPL36, BRIP1
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Entity ID: 12
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39S ribosomal protein L37, mitochondrialL [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37, MRPL2, RPML2, HSPC235
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Entity ID: 13
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39S ribosomal protein L38, mitochondrialM [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38, HSPC262
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Entity ID: 14
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39S ribosomal protein L39, mitochondrialN [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39, C21orf92, MRPL5, RPML5, MSTP003, PRED22
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Entity ID: 15
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39S ribosomal protein L40, mitochondrialO [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40, NLVCF, URIM
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Entity ID: 16
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39S ribosomal protein L41, mitochondrialP [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41, BMRP, MRPL27, RPML27, PIG3
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Entity ID: 19
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39S ribosomal protein L2, mitochondrialS [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2, CGI-22
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Entity ID: 20
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39S ribosomal protein L3, mitochondrialT [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3, MRL3, RPML3
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Entity ID: 21
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39S ribosomal protein L4, mitochondrialU [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4, CDABP0091, CGI-28
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Entity ID: 22
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39S ribosomal protein L9, mitochondrialV [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 23
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39S ribosomal protein L10, mitochondrialW [auth I]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10, MRPL8, RPML8
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Entity ID: 24
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39S ribosomal protein L11, mitochondrialX [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11, CGI-113
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39S ribosomal protein L13, mitochondrialY [auth K]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 26
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39S ribosomal protein L14, mitochondrialZ [auth L]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14, MRPL32, RPML32
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39S ribosomal protein L15, mitochondrialAA [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15, HSPC145
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39S ribosomal protein L16, mitochondrialBA [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16, PNAS-111
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39S ribosomal protein L17, mitochondrialCA [auth O]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17, LIP2
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Entity ID: 30
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39S ribosomal protein L18, mitochondrialDA [auth P]180Homo sapiensMutation(s): 0 
Gene Names: MRPL18, HSPC071
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Entity ID: 31
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39S ribosomal protein L19, mitochondrialEA [auth Q]292Homo sapiensMutation(s): 0 
Gene Names: MRPL19, KIAA0104, MRPL15
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39S ribosomal protein L20, mitochondrialFA [auth R]149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 33
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39S ribosomal protein L21, mitochondrialGA [auth S]205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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39S ribosomal protein L22, mitochondrialHA [auth T]206Homo sapiensMutation(s): 0 
Gene Names: MRPL22, MRPL25, RPML25, HSPC158
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Entity ID: 35
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39S ribosomal protein L23, mitochondrialIA [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23, L23MRP, RPL23L
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Entity ID: 36
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39S ribosomal protein L24, mitochondrialJA [auth V]216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 37
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39S ribosomal protein L27, mitochondrialKA [auth W]148Homo sapiensMutation(s): 0 
Gene Names: MRPL27, HSPC250
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Entity ID: 38
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39S ribosomal protein L28, mitochondrialLA [auth X]256Homo sapiensMutation(s): 0 
Gene Names: MRPL28, MAAT1
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Entity ID: 39
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39S ribosomal protein L47, mitochondrialMA [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47, NCM1, CGI-204
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Entity ID: 40
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39S ribosomal protein L30, mitochondrialNA [auth Z]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30, MRPL28, RPML28, HSPC249
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L42, mitochondrialOA [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42, MRPL31, MRPS32, RPML31, HSPC204, PTD007
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Entity ID: 42
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39S ribosomal protein L43, mitochondrialPA [auth b]215Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrialQA [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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Entity ID: 44
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39S ribosomal protein L45, mitochondrialRA [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondrialSA [auth e]279Homo sapiensMutation(s): 0 
Gene Names: MRPL46, C15orf4, LIECG2
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Entity ID: 46
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39S ribosomal protein L48, mitochondrialTA [auth f]212Homo sapiensMutation(s): 0 
Gene Names: MRPL48, CGI-118, HSPC290
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Entity ID: 47
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39S ribosomal protein L49, mitochondrialUA [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49, C11orf4, NOF1, OK/SW-cl.67
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Entity ID: 48
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39S ribosomal protein L50, mitochondrialVA [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 49
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39S ribosomal protein L51, mitochondrialWA [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51, MRP64, CDA09, HSPC241
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Entity ID: 50
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39S ribosomal protein L52, mitochondrialXA [auth j]123Homo sapiensMutation(s): 0 
Gene Names: MRPL52
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Find proteins for Q86TS9 (Homo sapiens)
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Entity ID: 51
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39S ribosomal protein L53, mitochondrialYA [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 52
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39S ribosomal protein L54, mitochondrialZA [auth l]138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Find proteins for Q6P161 (Homo sapiens)
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Entity ID: 53
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39S ribosomal protein L55, mitochondrialAB [auth m]128Homo sapiensMutation(s): 0 
Gene Names: MRPL55, UNQ5835/PRO19675
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Entity ID: 54
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Ribosomal protein 63, mitochondrialBB [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57, MRP63
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Find proteins for Q9BQC6 (Homo sapiens)
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Entity ID: 55
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Peptidyl-tRNA hydrolase ICT1, mitochondrialCB [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58, DS1, ICT1
EC: 3.1.1.29
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Find proteins for Q14197 (Homo sapiens)
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Entity ID: 56
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Growth arrest and DNA damage-inducible proteins-interacting protein 1DB [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1, MRPL59, PLINP1, PRG6
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Find proteins for Q8TAE8 (Homo sapiens)
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Entity ID: 57
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39S ribosomal protein S18a, mitochondrialEB [auth r]196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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Find proteins for Q9NVS2 (Homo sapiens)
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Entity ID: 58
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39S ribosomal protein S30, mitochondrialFB [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30, PDCD9, BM-047
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Find proteins for Q9NP92 (Homo sapiens)
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Entity ID: 17
MoleculeChainsLengthOrganismImage
16S mitochondrial rRNA, DNA (30-MER),16S mitochondrial rRNAQ [auth A]1,589Homo sapiens
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Entity ID: 18
MoleculeChainsLengthOrganismImage
mitochondrial tRNAValR [auth B]72Homo sapiens
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Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PM8
Query on PM8
Download Ideal Coordinates CCD File 
GB [auth w]S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE
C21 H41 N2 O7 P S
BPRKYNVKIAROET-IBGZPJMESA-N		 Ligand Interaction
SAM
Query on SAM
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HB [auth x]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N		 Ligand Interaction
N
Query on N
Download Ideal Coordinates CCD File 
ZE [auth A]ANY 5'-MONOPHOSPHATE NUCLEOTIDE
C5 H11 O7 P
CYZZKTRFOOKUMT-LMVFSUKVSA-N		 Ligand Interaction
FES
Query on FES
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DF [auth r]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
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IB [auth 0],
JB [auth 4]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
RE [auth A],
SE [auth A],
TE [auth A],
UE [auth A],
VE [auth A],
RE [auth A],
SE [auth A],
TE [auth A],
UE [auth A],
VE [auth A],
WE [auth A],
XE [auth A],
YE [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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AC [auth A],
AD [auth A],
AE [auth A],
AF [auth D],
BC [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth D],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth E],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth O],
DC [auth A],
DD [auth A],
DE [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
IC [auth A],
ID [auth A],
IE [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 A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
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],
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		 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
SAC
Query on SAC		Y [auth K]L-PEPTIDE LINKINGC5 H9 N O4SER
AYA
Query on AYA		IA [auth U]L-PEPTIDE LINKINGC5 H9 N O3ALA
THC
Query on THC		PA [auth b]L-PEPTIDE LINKINGC6 H11 N O4THR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.1

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_182341
European Molecular Biology Organization (EMBO)1074-2019
Swiss National Science Foundation182880

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-23
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references
  • Version 1.2: 2021-07-07
    Changes: Database references