7O9K

Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1, the MALSU module, GTPBP5 and mtEF-Tu


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 1.0 of the entry. See complete history


Literature

Structural basis for late maturation steps of the human mitoribosomal large subunit.

Cipullo, M.Gese, G.V.Khawaja, A.Hallberg, B.M.Rorbach, J.

(2021) Nat Commun 12: 3673-3673

  • DOI: https://doi.org/10.1038/s41467-021-23617-8
  • Primary Citation of Related Structures:  
    7O9K, 7O9M

  • PubMed Abstract: 
  • Mitochondrial ribosomes (mitoribosomes) synthesize a critical set of proteins essential for oxidative phosphorylation. Therefore, mitoribosomal function is vital to the cellular energy supply. Mitoribosome biogenesis follows distinct molecular pathways that remain poorly understood ...

    Mitochondrial ribosomes (mitoribosomes) synthesize a critical set of proteins essential for oxidative phosphorylation. Therefore, mitoribosomal function is vital to the cellular energy supply. Mitoribosome biogenesis follows distinct molecular pathways that remain poorly understood. Here, we determine the cryo-EM structures of mitoribosomes isolated from human cell lines with either depleted or overexpressed mitoribosome assembly factor GTPBP5, allowing us to capture consecutive steps during mitoribosomal large subunit (mt-LSU) biogenesis. Our structures provide essential insights into the last steps of 16S rRNA folding, methylation and peptidyl transferase centre (PTC) completion, which require the coordinated action of nine assembly factors. We show that mammalian-specific MTERF4 contributes to the folding of 16S rRNA, allowing 16 S rRNA methylation by MRM2, while GTPBP5 and NSUN4 promote fine-tuning rRNA rearrangements leading to PTC formation. Moreover, our data reveal an unexpected involvement of the elongation factor mtEF-Tu in mt-LSU assembly, where mtEF-Tu interacts with GTPBP5, similar to its interaction with tRNA during translational elongation.


    Organizational Affiliation

    Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden. joanna.rorbach@ki.se.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialA [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
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Entity ID: 2
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39S ribosomal protein L42, mitochondrialB [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialC [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrialD [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialE [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
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Entity ID: 6
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39S ribosomal protein L36, mitochondrialF [auth 4]103Homo sapiensMutation(s): 0 
Gene Names: MRPL36BRIP1
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Entity ID: 7
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39S ribosomal protein L37, mitochondrialG [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
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Entity ID: 8
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39S ribosomal protein L38, mitochondrialH [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
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Entity ID: 9
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39S ribosomal protein L39, mitochondrialI [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
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Entity ID: 10
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39S ribosomal protein L40, mitochondrialJ [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
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Entity ID: 11
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39S ribosomal protein L41, mitochondrialK [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
5-methylcytosine rRNA methyltransferase NSUN4M [auth A1]384Homo sapiensMutation(s): 0 
Gene Names: NSUN4
EC: 2.1.1
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Entity ID: 15
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Transcription termination factor 4, mitochondrialO [auth A2]381Homo sapiensMutation(s): 0 
Gene Names: MTERF4MTERFD2HSPC096
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Entity ID: 16
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Mitochondrial ribosome-associated GTPase 1P [auth C]334Homo sapiensMutation(s): 0 
Gene Names: MTG1GTPBP7
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Entity ID: 17
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39S ribosomal protein L2, mitochondrialQ [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
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Entity ID: 18
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39S ribosomal protein L3, mitochondrialR [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3MRL3RPML3
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Entity ID: 19
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39S ribosomal protein L4, mitochondrialS [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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Entity ID: 20
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39S ribosomal protein L12, mitochondrial198Homo sapiensMutation(s): 0 
Gene Names: MRPL12MRPL7RPML12
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Entity ID: 21
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Mitochondrial ribosome-associated GTPase 2U [auth G]414Homo sapiensMutation(s): 0 
Gene Names: MTG2GTPBP5OBGH1
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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: MRPL10MRPL8RPML8
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Entity ID: 24
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39S ribosomal protein L11, mitochondrialX [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11CGI-113
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Entity ID: 25
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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: MRPL14MRPL32RPML32
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Entity ID: 27
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39S ribosomal protein L15, mitochondrialAA [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
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Entity ID: 28
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39S ribosomal protein L16, mitochondrialBA [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
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Entity ID: 29
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39S ribosomal protein L17, mitochondrialCA [auth O]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17LIP2
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Entity ID: 30
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Mitochondrial ribosomal protein L18, isoform CRA_bDA [auth P]179Homo sapiensMutation(s): 0 
Gene Names: MRPL18hCG_34030
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Entity ID: 31
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39S ribosomal protein L19, mitochondrialEA [auth Q]292Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
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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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Entity ID: 34
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39S ribosomal protein L22, mitochondrialHA [auth T]212Homo sapiensMutation(s): 0 
Gene Names: MRPL22
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Entity ID: 35
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39S ribosomal protein L23, mitochondrialIA [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
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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: MRPL27HSPC250
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Entity ID: 38
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39S ribosomal protein L28, mitochondrialLA [auth X]256Homo sapiensMutation(s): 0 
Gene Names: MRPL28MAAT1
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Entity ID: 39
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39S ribosomal protein L47, mitochondrialMA [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-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: MRPL30MRPL28RPML28HSPC249
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Entity ID: 41
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39S ribosomal protein L43, mitochondrialOA [auth b]215Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrialPA [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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Entity ID: 43
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39S ribosomal protein L45, mitochondrialQA [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 44
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39S ribosomal protein L46, mitochondrialRA [auth e]279Homo sapiensMutation(s): 0 
Gene Names: MRPL46C15orf4LIECG2
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Entity ID: 45
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39S ribosomal protein L48, mitochondrialSA [auth f]212Homo sapiensMutation(s): 0 
Gene Names: MRPL48CGI-118HSPC290
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Entity ID: 46
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39S ribosomal protein L49, mitochondrialTA [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
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Entity ID: 47
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39S ribosomal protein L50, mitochondrialUA [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 48
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39S ribosomal protein L51, mitochondrialVA [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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Entity ID: 49
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39S ribosomal protein L52, mitochondrialWA [auth j]123Homo sapiensMutation(s): 0 
Gene Names: MRPL52
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Entity ID: 50
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39S ribosomal protein L53, mitochondrialXA [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 51
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39S ribosomal protein L54, mitochondrialYA [auth l]138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 52
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39S ribosomal protein L55, mitochondrialZA [auth m]128Homo sapiensMutation(s): 0 
Gene Names: MRPL55UNQ5835/PRO19675
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Entity ID: 53
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rRNA methyltransferase 2, mitochondrialAB [auth n]246Homo sapiensMutation(s): 0 
Gene Names: MRM2FJH1FTSJ2
EC: 2.1.1
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Entity ID: 54
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Ribosomal protein 63, mitochondrialBB [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialCB [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
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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: GADD45GIP1MRPL59PLINP1PRG6
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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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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialFB [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor Tu, mitochondrialGB [auth t]452Homo sapiensMutation(s): 0 
Gene Names: TUFM
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Entity ID: 60
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Mitochondrial assembly of ribosomal large subunit protein 1NB [auth u]234Homo sapiensMutation(s): 0 
Gene Names: MALSU1C7orf30
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Entity ID: 61
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MIEF1 upstream open reading frame proteinOB [auth v]70Homo sapiensMutation(s): 0 
Gene Names: MIEF1
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Entity ID: 62
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Acyl carrier protein, mitochondrialPB [auth w]156Homo sapiensMutation(s): 0 
Gene Names: NDUFAB1
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
UNKQB [auth UNK]28Homo sapiensMutation(s): 0 
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Entity ID: 12
MoleculeChainsLengthOrganismImage
16S rRNAL [auth A]1,559Homo sapiens
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Entity ID: 14
MoleculeChainsLengthOrganismImage
MT-TRNAVALN [auth B]69Homo sapiens
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Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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FF [auth G]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
GDP
Query on GDP

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BF [auth C],
LF [auth t]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SAM
Query on SAM

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AF [auth A1]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
SAH
Query on SAH

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KF [auth n]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
PNS
Query on PNS

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NF [auth w]4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
ZN
Query on ZN

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RB [auth 0],
SB [auth 4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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],
CF [auth D],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth E],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth G],
FC [auth A],
FD [auth A],
FE [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth G],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth M],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth W],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth g],
KC [auth A],
KD [auth A],
KE [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth t],
NC [auth A],
ND [auth A],
NE [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.15
MODEL REFINEMENTREFMAC5.8.0267

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release