7QH6

Cryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 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

A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit.

Rebelo-Guiomar, P.Pellegrino, S.Dent, K.C.Sas-Chen, A.Miller-Fleming, L.Garone, C.Van Haute, L.Rogan, J.F.Dinan, A.Firth, A.E.Andrews, B.Whitworth, A.J.Schwartz, S.Warren, A.J.Minczuk, M.

(2022) Nat Commun 13: 929-929

  • DOI: 10.1038/s41467-022-28503-5
  • Primary Citation of Related Structures:  
    7QH6, 7QH7

  • PubMed Abstract: 
  • Many cellular processes, including ribosome biogenesis, are regulated through post-transcriptional RNA modifications. Here, a genome-wide analysis of the human mitochondrial transcriptome shows that 2'-O-methylation is limited to residues of the mitoribosomal large subunit (mtLSU) 16S mt-rRNA, introduced by MRM1, MRM2 and MRM3, with the modifications installed by the latter two proteins being interdependent ...

    Many cellular processes, including ribosome biogenesis, are regulated through post-transcriptional RNA modifications. Here, a genome-wide analysis of the human mitochondrial transcriptome shows that 2'-O-methylation is limited to residues of the mitoribosomal large subunit (mtLSU) 16S mt-rRNA, introduced by MRM1, MRM2 and MRM3, with the modifications installed by the latter two proteins being interdependent. MRM2 controls mitochondrial respiration by regulating mitoribosome biogenesis. In its absence, mtLSU particles (visualized by cryo-EM at the resolution of 2.6 Å) present disordered RNA domains, partial occupancy of bL36m and bound MALSU1:L0R8F8:mtACP anti-association module, allowing five mtLSU biogenesis intermediates with different intersubunit interface configurations to be placed along the assembly pathway. However, mitoribosome biogenesis does not depend on the methyltransferase activity of MRM2. Disruption of the MRM2 Drosophila melanogaster orthologue leads to mitochondria-related developmental arrest. This work identifies a key checkpoint during mtLSU assembly, essential to maintain mitochondrial homeostasis.


    Organizational Affiliation

    MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Hills Rd, Cambridge, CB2 0XY, UK. michal.minczuk@mrc-mbu.cam.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialA [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
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Entity ID: 2
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39S ribosomal protein L3, mitochondrialB [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3MRL3RPML3
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialC [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialD [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 5
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39S ribosomal protein L13, mitochondrialE [auth K]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 6
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39S ribosomal protein L14, mitochondrialF [auth L]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14MRPL32RPML32
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Entity ID: 7
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39S ribosomal protein L15, mitochondrialG [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
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Entity ID: 8
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39S ribosomal protein L16, mitochondrialH [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
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Entity ID: 9
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39S ribosomal protein L17, mitochondrialI [auth O]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17LIP2
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Entity ID: 10
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39S ribosomal protein L18, mitochondrialJ [auth P]180Homo sapiensMutation(s): 0 
Gene Names: MRPL18HSPC071
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Entity ID: 11
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39S ribosomal protein L19, mitochondrialK [auth Q]292Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
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39S ribosomal protein L20, mitochondrialL [auth R]149Homo sapiensMutation(s): 0 
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39S ribosomal protein L21, mitochondrialM [auth S]205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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39S ribosomal protein L22, mitochondrialN [auth T]206Homo sapiensMutation(s): 0 
Gene Names: MRPL22MRPL25RPML25HSPC158
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Entity ID: 15
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39S ribosomal protein L23, mitochondrialO [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
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Entity ID: 16
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39S ribosomal protein L24, mitochondrialP [auth V]216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 17
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39S ribosomal protein L27, mitochondrialQ [auth W]148Homo sapiensMutation(s): 0 
Gene Names: MRPL27HSPC250
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Entity ID: 18
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39S ribosomal protein L28, mitochondrialR [auth X]256Homo sapiensMutation(s): 0 
Gene Names: MRPL28MAAT1
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Entity ID: 19
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39S ribosomal protein L47, mitochondrialS [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-204
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Entity ID: 20
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39S ribosomal protein L30, mitochondrialT [auth Z]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30MRPL28RPML28HSPC249
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Entity ID: 21
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39S ribosomal protein L32, mitochondrialU [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
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Entity ID: 22
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39S ribosomal protein L33, mitochondrialV [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
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Entity ID: 23
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39S ribosomal protein L34, mitochondrialW [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 24
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39S ribosomal protein L35, mitochondrialX [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
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39S ribosomal protein L37, mitochondrialY [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
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39S ribosomal protein L38, mitochondrialZ [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
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Entity ID: 27
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39S ribosomal protein L39, mitochondrialAA [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
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Entity ID: 28
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39S ribosomal protein L41, mitochondrialBA [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
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39S ribosomal protein L42, mitochondrialCA [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
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39S ribosomal protein L43, mitochondrialDA [auth b]215Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 31
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39S ribosomal protein L44, mitochondrialEA [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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Entity ID: 32
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39S ribosomal protein L45, mitochondrialFA [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 33
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39S ribosomal protein L49, mitochondrialGA [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
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Entity ID: 34
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39S ribosomal protein L50, mitochondrialHA [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 35
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39S ribosomal protein L51, mitochondrialIA [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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39S ribosomal protein L52, mitochondrialJA [auth j]123Homo sapiensMutation(s): 0 
Gene Names: MRPL52
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Entity ID: 37
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Ribosomal protein 63, mitochondrialKA [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
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Entity ID: 38
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Peptidyl-tRNA hydrolase ICT1, mitochondrialLA [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
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Find proteins for Q14197 (Homo sapiens)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1MA [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S18a, mitochondrialNA [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: 41
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialOA [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
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Find proteins for Q9NP92 (Homo sapiens)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial assembly of ribosomal large subunit protein 1PA [auth u]234Homo sapiensMutation(s): 0 
Gene Names: MALSU1C7orf30
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
MIEF1 upstream open reading frame proteinQA [auth v]70Homo sapiensMutation(s): 0 
Gene Names: MIEF1
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialRA [auth w]156Homo sapiensMutation(s): 0 
Gene Names: NDUFAB1
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Find proteins for O14561 (Homo sapiens)
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Entity ID: 45
MoleculeChainsLengthOrganismImage
16S ribosomal RNASA [auth A]1,559Homo sapiens
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Entity ID: 46
MoleculeChainsLengthOrganismImage
mitochondrial tRNAValTA [auth B]69Homo sapiens
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
UA [auth 0]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00015/4

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release