9HCH image
Deposition Date 2024-11-10
Release Date 2025-06-18
Last Version Date 2025-07-09
Entry Detail
PDB ID:
9HCH
Keywords:
RIBOSOME
Title:
Mouse mitoribosome large subunit assembly intermediate bound to NSUN4, METRF4, GTPBP7 and the MALSU1-L0R8F8-mt-ACP complex, State C1 (SAMC knock-out)
Biological Source:
Source Organism:
Mus musculus (Taxon ID: 10090)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.85 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9HCH validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL32m
Gene (Uniprot):Mrpl32
Chain IDs:Z (auth: 0)
Chain Length:187
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9DCI9 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33m
Gene (Uniprot):Mrpl33
Chain IDs:AA (auth: 1)
Chain Length:65
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CQP0 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34m
Gene (Uniprot):Mrpl34
Chain IDs:BA (auth: 2)
Chain Length:92
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q99N91 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL35m
Gene (Uniprot):Mrpl35
Chain IDs:CA (auth: 3)
Chain Length:188
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CQL6 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL36m
Gene (Uniprot):Mrpl36
Chain IDs:DA (auth: 4)
Chain Length:101
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q99N90 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL37
Gene (Uniprot):Mrpl37
Chain IDs:XA (auth: 5)
Chain Length:423
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q921S7 Pfam ID:PF07147
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL38
Gene (Uniprot):Mrpl38
Chain IDs:EA (auth: 6)
Chain Length:380
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q8K2M0 Pfam ID:PF01161
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL39
Gene (Uniprot):Mrpl39
Chain IDs:FA (auth: 7)
Chain Length:336
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9JKF7
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL40
Gene (Uniprot):Mrpl40
Chain IDs:YA (auth: 8)
Chain Length:206
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9Z2Q5 Pfam ID:PF09812
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL41
Gene (Uniprot):Mrpl41
Chain IDs:ZA (auth: 9)
Chain Length:135
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CQN7 Pfam ID:PF09809
Polymer Type:polyribonucleotide
Molecule:16S rRNA (1584-MER)
Chain IDs:A
Chain Length:1584
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polyribonucleotide
Molecule:tRNA-Phe (68-MER)
Chain IDs:B
Chain Length:159
Number of Molecules:1
Biological Source:Mus musculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2m
Gene (Uniprot):Mrpl2
Chain IDs:C (auth: D)
Chain Length:246
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9D773 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3m
Gene (Uniprot):Mrpl3
Chain IDs:D (auth: E)
Chain Length:348
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q99N95 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4m
Gene (Uniprot):Mrpl4
Chain IDs:E (auth: F)
Chain Length:294
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9DCU6 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL9m
Gene (Uniprot):Mrpl9
Chain IDs:F (auth: H)
Chain Length:265
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q99N94 Pfam ID:PF01281, PF22078
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL10m
Gene (Uniprot):Mrpl10
Chain IDs:G (auth: I)
Chain Length:128
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q3TBW2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL11m
Gene (Uniprot):Mrpl11
Chain IDs:H (auth: J)
Chain Length:121
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CQF0 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13m
Gene (Uniprot):Mrpl13
Chain IDs:I (auth: K)
Chain Length:118
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9D1P0 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14m
Gene (Uniprot):Mrpl14
Chain IDs:J (auth: L)
Chain Length:135
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9D1I6 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15m
Gene (Uniprot):Mrpl15
Chain IDs:K (auth: M)
Chain Length:127
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CPR5 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16m
Gene (Uniprot):Mrpl16
Chain IDs:L (auth: N)
Chain Length:251
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q99N93 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL17m
Gene (Uniprot):Mrpl17
Chain IDs:M (auth: O)
Chain Length:176
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9D8P4 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18m
Gene (Uniprot):Mrpl18
Chain IDs:N (auth: P)
Chain Length:206
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CQL5 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL19m
Gene (Uniprot):Mrpl19
Chain IDs:O (auth: Q)
Chain Length:292
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9D338 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL20m
Gene (Uniprot):Mrpl20
Chain IDs:P (auth: R)
Chain Length:196
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CQL4 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL21m
Gene (Uniprot):Mrpl21
Chain IDs:Q (auth: S)
Chain Length:442
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9D1N9 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22m
Gene (Uniprot):Mrpl22
Chain IDs:R (auth: T)
Chain Length:206
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q8BU88 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23m
Gene (Uniprot):Mrpl23
Chain IDs:S (auth: U)
Chain Length:228
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:O35972 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24m
Gene (Uniprot):Mrpl24
Chain IDs:T (auth: V)
Chain Length:70
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CQ06 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27m
Gene (Uniprot):Mrpl27
Chain IDs:U (auth: W)
Chain Length:156
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q99N92 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL28m,Large ribosomal subunit protein bL32m
Gene (Uniprot):Mrpl28, Mrpl32
Chain IDs:V (auth: X)
Chain Length:294
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9D1B9,Q9DCI9 Pfam ID:PF01783, PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29m
Gene (Uniprot):Mrpl47
Chain IDs:W (auth: Y)
Chain Length:346
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q8K2Y7 Pfam ID:PF06984
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30m
Gene (Uniprot):Mrpl30
Chain IDs:X (auth: Z)
Chain Length:160
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9D7N6 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL42
Gene (Uniprot):Mrpl42
Chain IDs:AB (auth: a)
Chain Length:1584
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CPV3 Pfam ID:PF10210
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL43
Gene (Uniprot):Mrpl43
Chain IDs:GA (auth: b)
Chain Length:159
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q5RL20 Pfam ID:PF05047
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL44
Gene (Uniprot):Mrpl44
Chain IDs:HA (auth: c)
Chain Length:308
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CY73 Pfam ID:PF22935, PF22892
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL45
Gene (Uniprot):Mrpl45
Chain IDs:IA (auth: d)
Chain Length:246
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9D0Q7 Pfam ID:PF04280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL46
Gene (Uniprot):Mrpl46
Chain IDs:JA (auth: e)
Chain Length:348
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9EQI8 Pfam ID:PF11788
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL48
Gene (Uniprot):Mrpl48
Chain IDs:KA (auth: f)
Chain Length:294
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q8JZS9 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL49
Gene (Uniprot):Mrpl49
Chain IDs:LA (auth: g)
Chain Length:166
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CQ40 Pfam ID:PF05046
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL50
Gene (Uniprot):Mrpl50
Chain IDs:MA (auth: h)
Chain Length:265
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q8VDT9 Pfam ID:PF10501
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL51
Gene (Uniprot):Mrpl51
Chain IDs:NA (auth: i)
Chain Length:128
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CPY1 Pfam ID:PF10244
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL52
Gene (Uniprot):Mrpl52
Chain IDs:OA (auth: j)
Chain Length:121
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9D0Y8 Pfam ID:PF18699
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL53
Gene (Uniprot):Mrpl53
Chain IDs:FB (auth: k)
Chain Length:118
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9D1H8 Pfam ID:PF10780
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL54
Gene (Uniprot):Mrpl54
Chain IDs:CB (auth: l)
Chain Length:135
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CPW3 Pfam ID:PF08561
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL55
Gene (Uniprot):Mrpl55
Chain IDs:BB (auth: m)
Chain Length:127
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CZ83 Pfam ID:PF09776
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL63
Gene (Uniprot):Mrpl57
Chain IDs:PA (auth: o)
Chain Length:176
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CQF8 Pfam ID:PF14978
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL62
Gene (Uniprot):Mrpl58
Chain IDs:QA (auth: p)
Chain Length:206
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q8R035 Pfam ID:PF00472
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL64
Gene (Uniprot):Gadd45gip1
Chain IDs:RA (auth: q)
Chain Length:292
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CR59 Pfam ID:PF10147
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL66
Gene (Uniprot):Mrps18a
Chain IDs:SA (auth: r)
Chain Length:196
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q99N85 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL65
Gene (Uniprot):Mrps30
Chain IDs:TA (auth: s)
Chain Length:442
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9D0G0 Pfam ID:PF07147
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial assembly of ribosomal large subunit protein 1
Gene (Uniprot):Malsu1
Chain IDs:UA (auth: u)
Chain Length:228
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CWV0 Pfam ID:PF02410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Predicted gene, 55359
Gene (Uniprot):Gm55359
Chain IDs:VA (auth: v)
Chain Length:70
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:A0A2I3BQS8 Pfam ID:PF05347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein, mitochondrial
Gene (Uniprot):Ndufab1
Chain IDs:WA (auth: w)
Chain Length:156
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CR21 Pfam ID:PF00550
Protein Blast
Polymer Type:polypeptide(L)
Molecule:5-cytosine rRNA methyltransferase NSUN4
Gene (Uniprot):Nsun4
Chain IDs:Y (auth: x)
Chain Length:294
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CZ57 Pfam ID:PF01189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription termination factor 4, mitochondrial
Gene (Uniprot):Mterf4
Chain IDs:EB (auth: y)
Chain Length:346
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q8BVN4 Pfam ID:PF02536
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosome-associated GTPase 1
Gene (Uniprot):Mtg1
Chain IDs:DB (auth: z)
Chain Length:160
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q8R2R6 Pfam ID:PF01926
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
PSU A U modified residue
Ligand Molecules
FES
GNP
MG
ZN
Primary Citation
The mitochondrial methylation potential gates mitoribosome assembly.
Nat Commun 16 5388 5388 (2025)
PMID: 40562754 DOI: 10.1038/s41467-025-60977-x

Abstact

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.

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Protein

Chemical

Disease

Primary Citation of related structures
9HCC
9HCD
9HCE
9HCF
9E9C
9HCG