ISDA

Deposition Date 2024-11-08

Release Date 2025-07-09

Last Version Date 2025-07-09

Entry Detail

PDB ID:

9HCF

Keywords:

RIBOSOME

Title:

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)

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

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL32m
Gene (Uniprot):Mrpl32
Chain IDs:CB (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:Z (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:AA (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:BA (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:CA (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:QA (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:DA (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:EA (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:RA (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:SA (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 (1432-MER)
Chain IDs:A
Chain Length:142
Number of Molecules:1
Biological Source:Mus musculus

Polymer Type:polyribonucleotide
Molecule:RNA (63-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:283
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:211
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:295
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:222
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:149
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:209
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:146
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:148
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:TA (auth: a)
Chain Length:142
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:FA (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:ZA (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:DB (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:EB (auth: e)
Chain Length:283
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:GA (auth: f)
Chain Length:211
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:AB (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:HA (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:IA (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:JA (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:BB (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:WA (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:UA (auth: m)
Chain Length:295
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:KA (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:FB (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:LA (auth: q)
Chain Length:222
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:MA (auth: r)
Chain Length:149
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:NA (auth: s)
Chain Length:209
Number of Molecules:1
Biological Source:Mus musculus

UniProt ID:Q9D0G0 Pfam ID:PF07147

Protein Blast

Polymer Type:polypeptide(L)
Molecule:GTP-binding protein 10
Gene (Uniprot):Gtpbp10
Chain IDs:GB (auth: t)
Chain Length:206
Number of Molecules:1
Biological Source:Mus musculus

UniProt ID:Q8K013 Pfam ID:PF01018, PF01926

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial assembly of ribosomal large subunit protein 1
Gene (Uniprot):Malsu1
Chain IDs:OA (auth: u)
Chain Length:146
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:PA (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:YA (auth: w)
Chain Length:148
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:XA (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:VA (auth: z)
Chain Length:160
Number of Molecules:1
Biological Source:Mus musculus

UniProt ID:Q8R2R6 Pfam ID:PF01926

Ligand Molecules

FES

GNP

Primary Citation

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.Show

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures