9HCD | pdb_00009hcd

Mouse mitoribosome large subunit assembly intermediate (with uL16m) bound to MRM3-dimer, DDX28 and the MALSU-L0R8F8-mt-ACP complex, state A2 (SAMC knock-out)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.63 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

The mitochondrial methylation potential gates mitoribosome assembly.

Glasgow, R.I.C., Singh, V., Pena-Perez, L., Wilhalm, A., Moedas, M.F., Moore, D., Rosenberger, F.A., Li, X., Atanassov, I., Saba, M., Cipullo, M., Rorbach, J., Wedell, A., Freyer, C., Amunts, A., Wredenberg, A.

(2025) Nat Commun 16: 5388-5388

  • DOI: https://doi.org/10.1038/s41467-025-60977-x
  • Primary Citation of Related Structures:  
    9E9C, 9HCC, 9HCD, 9HCE, 9HCF, 9HCG, 9HCH

  • PubMed Abstract: 

    S-adenosylmethionine (SAM) is the principal methyl donor in cells and is essential for mitochondrial gene expression, influencing RNA modifications, translation, and ribosome biogenesis. Using direct long-read RNA sequencing in mouse tissues and embryonic fibroblasts, we show that processing of the mitochondrial ribosomal gene cluster fails in the absence of mitochondrial SAM, leading to an accumulation of unprocessed precursors. Proteomic analysis of ribosome fractions revealed these precursors associated with processing and assembly factors, indicating stalled biogenesis. Structural analysis by cryo-electron microscopy demonstrated that SAM-dependent methylation is required for peptidyl transferase centre formation during mitoribosome assembly. Our findings identify a critical role for SAM in coordinating mitoribosomal RNA processing and large subunit maturation, linking cellular methylation potential to mitochondrial translation capacity.

    • Organizational Affiliation: 
    • Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2mC [auth D]246Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3mD [auth E]348Mus musculusMutation(s): 0 
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IMPC:  MGI:2137204
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4mE [auth F]294Mus musculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9mF [auth H]268Mus musculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL10mG [auth I]262Mus musculusMutation(s): 0 
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IMPC:  MGI:1333801
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL11mH [auth J]192Mus musculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13mI [auth K]178Mus musculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14mJ [auth L]145Mus musculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15mK [auth M]295Mus musculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16mL [auth N]251Mus musculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17mM [auth O]176Mus musculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18mN [auth P]180Mus musculusMutation(s): 0 
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IMPC:  MGI:1914931
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19mO [auth Q]292Mus musculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20mP [auth R]149Mus musculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21mQ [auth S]209Mus musculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22mR [auth T]206Mus musculusMutation(s): 0 
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IMPC:  MGI:1333794
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23mS [auth U]146Mus musculusMutation(s): 0 
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IMPC:  MGI:1196612
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24mT [auth V]216Mus musculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28m,Large ribosomal subunit protein bL32mU [auth X]294Mus musculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29mV [auth Y]252Mus musculusMutation(s): 0 
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IMPC:  MGI:1921850
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30mW [auth Z]160Mus musculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32mX [auth 0]187Mus musculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL37Y [auth 5]423Mus musculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL38Z [auth 6]380Mus musculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL39AA [auth 7]336Mus musculusMutation(s): 0 
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IMPC:  MGI:1351620
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL40BA [auth 8]206Mus musculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL41CA [auth 9]135Mus musculusMutation(s): 0 
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IMPC:  MGI:1333816
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL42DA [auth a]142Mus musculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL43EA [auth b]159Mus musculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL44FA [auth c]308Mus musculusMutation(s): 0 
EC: 3.1.26
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IMPC:  MGI:1916413
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL45GA [auth d]306Mus musculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL46HA [auth e]283Mus musculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL48IA [auth f]211Mus musculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL49JA [auth g]166Mus musculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL50KA [auth h]159Mus musculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL51LA [auth i]128Mus musculusMutation(s): 0 
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IMPC:  MGI:1913743
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL52MA [auth j]121Mus musculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL53NA [auth k]118Mus musculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL54OA [auth l]135Mus musculusMutation(s): 0 
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IMPC:  MGI:1913297
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL63PA [auth o]102Mus musculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL62QA [auth p]206Mus musculusMutation(s): 0 
EC: 3.1.1.29
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IMPC:  MGI:1915822
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL64RA [auth q]222Mus musculusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL66SA [auth r]196Mus musculusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL65TA [auth s]442Mus musculusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial assembly of ribosomal large subunit protein 1UA [auth u]228Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CWV0 (Mus musculus)
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UniProt GroupQ9CWV0
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Predicted gene, 55359VA [auth v]70Mus musculusMutation(s): 0 
UniProt
Find proteins for A0A2I3BQS8 (Mus musculus)
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UniProt GroupA0A2I3BQS8
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialWA [auth w]156Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CR21 (Mus musculus)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA methyltransferase 3, mitochondrialXA [auth x],
YA [auth y]		418Mus musculusMutation(s): 0 
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5ND52 (Mus musculus)
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IMPC:  MGI:1914640
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX28ZA [auth z]540Mus musculusMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for Q9CWT6 (Mus musculus)
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNA (1584-MER)1,584Mus musculus
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Entity ID: 2
MoleculeChains LengthOrganismImage
tRNA-Phe (68-MER)68Mus musculus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--
Novo Nordisk FoundationDenmark--
Knut and Alice Wallenberg FoundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-16
    Changes: Data collection