9HCF | pdb_00009hcf

Mouse mitoribosome large subunit assembly intermediate bound to NSUN4, METRF4, GTPBP7, GTPBP10 and the MALSU-L0R8F8-mtACP complex with uL16m, State B2 (SAMC knock-out)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    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]265Mus 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 bL27mU [auth W]148Mus musculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28m,Large ribosomal subunit protein bL32mV [auth X]294Mus musculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29mW [auth Y]252Mus musculusMutation(s): 0 
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IMPC:  MGI:1921850
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30mX [auth Z]160Mus musculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
5-cytosine rRNA methyltransferase NSUN4Y [auth x]381Mus musculusMutation(s): 0 
EC: 2.1.1
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33mZ [auth 1]65Mus musculusMutation(s): 0 
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IMPC:  MGI:2137225
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34mAA [auth 2]92Mus musculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL35mBA [auth 3]188Mus musculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL36mCA [auth 4]101Mus musculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL38DA [auth 6]380Mus musculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL39EA [auth 7]336Mus musculusMutation(s): 0 
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IMPC:  MGI:1351620
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL43FA [auth b]159Mus musculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL48GA [auth f]211Mus musculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL50HA [auth h]159Mus musculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL51IA [auth i]128Mus musculusMutation(s): 0 
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IMPC:  MGI:1913743
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL52JA [auth j]121Mus musculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL63KA [auth o]102Mus musculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL64LA [auth q]222Mus musculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL66MA [auth r]196Mus musculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL65NA [auth s]442Mus musculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial assembly of ribosomal large subunit protein 1OA [auth u]228Mus musculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Predicted gene, 55359PA [auth v]70Mus musculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL37QA [auth 5]423Mus musculusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL40RA [auth 8]206Mus musculusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL41SA [auth 9]135Mus musculusMutation(s): 0 
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IMPC:  MGI:1333816
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL42TA [auth a]142Mus musculusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL55UA [auth m]127Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CZ83 (Mus musculus)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosome-associated GTPase 1VA [auth z]326Mus musculusMutation(s): 0 
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IMPC:  MGI:2685015
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UniProt GroupQ8R2R6
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL54WA [auth l]135Mus musculusMutation(s): 0 
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IMPC:  MGI:1913297
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination factor 4, mitochondrialXA [auth y]346Mus musculusMutation(s): 0 
UniProt
Find proteins for Q8BVN4 (Mus musculus)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialYA [auth w]156Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CR21 (Mus musculus)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL44ZA [auth c]308Mus musculusMutation(s): 0 
EC: 3.1.26
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Find proteins for Q9CY73 (Mus musculus)
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IMPC:  MGI:1916413
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL49AB [auth g]166Mus musculusMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL53BB [auth k]118Mus musculusMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32mCB [auth 0]187Mus musculusMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL45DB [auth d]306Mus musculusMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL46EB [auth e]283Mus musculusMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL62FB [auth p]206Mus musculusMutation(s): 0 
EC: 3.1.1.29
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IMPC:  MGI:1915822
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein 10GB [auth t]366Mus musculusMutation(s): 0 
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IMPC:  MGI:2385599
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNA (1432-MER)1,584Mus musculus
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (63-MER)68Mus musculus
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
EF [auth z],
GF [auth t]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
FES
Query on FES

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ZE [auth I]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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DF [auth 4],
FF [auth 0]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth A]
AD [auth A]
AE [auth A]
AF [auth M]
BC [auth A]
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth M],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth O],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth R],
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],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
JB [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],
RE [auth A],
SB [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]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



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: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection