9GYT image
Deposition Date 2024-10-02
Release Date 2025-10-15
Last Version Date 2025-12-17
Entry Detail
PDB ID:
9GYT
Keywords:
RIBOSOME
Title:
High resolution structure of B. oleracea mitoribosome
Biological Source:
Source Organism(s):
Brassica oleracea var. botrytis (Taxon ID: 3715)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.11 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9GYT validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:26S rRNA
Chain IDs:HC (auth: 1)
Chain Length:2922
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2 C-terminal domain-containing protein
Chain IDs:NA (auth: 1B)
Chain Length:217
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3B6N5 Pfam ID:PF03947
Polymer Type:polypeptide(L)
Molecule:uL2m N-ter mitochondrial
Chain IDs:OA (auth: 1C)
Chain Length:135
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:uL3m
Chain IDs:PA (auth: 1D)
Chain Length:139
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:uL4m
Chain IDs:QA (auth: 1E)
Chain Length:106
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:uL5m
Chain IDs:RA (auth: 1F)
Chain Length:146
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6 alpha-beta domain-containing protein
Chain IDs:SA (auth: 1G)
Chain Length:102
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3D316 Pfam ID:PF00347
Polymer Type:polypeptide(L)
Molecule:bL9m
Chain IDs:TA (auth: 1H)
Chain Length:220
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:uL10m
Chain IDs:UA (auth: 1I)
Chain Length:170
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:uL11m
Chain IDs:VA (auth: 1J)
Chain Length:90
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:WA (auth: 1K)
Chain Length:204
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3B978 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL14m
Chain IDs:XA (auth: 1L)
Chain Length:176
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3D9E7 Pfam ID:PF00238
Polymer Type:polypeptide(L)
Molecule:uL15m
Chain IDs:YA (auth: 1M)
Chain Length:128
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16m
Gene (Uniprot):RPL16
Chain IDs:ZA (auth: 1N)
Chain Length:179
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:Q95747 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):F2Q70_00000589
Chain IDs:AB (auth: 1O)
Chain Length:160
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A8S9IRX0 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L18e/L15P domain-containing protein
Chain IDs:BB (auth: 1P)
Chain Length:130
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3DCH7 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:bL19m
Chain IDs:CB (auth: 1Q)
Chain Length:78
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3B0P2 Pfam ID:PF01245
Polymer Type:polypeptide(L)
Molecule:bL20m
Chain IDs:DB (auth: 1R)
Chain Length:126
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:bL21m
Chain IDs:EB (auth: 1S)
Chain Length:270
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22m
Chain IDs:FB (auth: 1T)
Chain Length:491
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3BFS0 Pfam ID:PF00237
Polymer Type:polypeptide(L)
Molecule:uL23m
Chain IDs:GB (auth: 1U)
Chain Length:180
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:uL24m
Chain IDs:HB (auth: 1V)
Chain Length:514
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:bL25-2m
Chain IDs:IB (auth: 1W)
Chain Length:248
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:bL25m
Chain IDs:JB (auth: 1X)
Chain Length:271
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3BK40 Pfam ID:PF01386, PF14693
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:KB (auth: 1Y)
Chain Length:156
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3B184 Pfam ID:PF01016
Polymer Type:polypeptide(L)
Molecule:bL28m
Chain IDs:LB (auth: 1Z)
Chain Length:215
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:uL29m
Chain IDs:MB (auth: 1a)
Chain Length:144
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:uL30m
Chain IDs:NB (auth: 1b)
Chain Length:217
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:bL31m
Chain IDs:OB (auth: 1c)
Chain Length:135
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:bL32m
Chain IDs:PB (auth: 1d)
Chain Length:139
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:bL33m
Chain IDs:QB (auth: 1e)
Chain Length:106
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34m
Chain IDs:RB (auth: 1f)
Chain Length:146
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3CKG1 Pfam ID:PF00468
Polymer Type:polypeptide(L)
Molecule:bL35m
Chain IDs:SB (auth: 1g)
Chain Length:102
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein
Gene (Uniprot):F5O24.70, F5O24_70
Chain IDs:TB (auth: 1h)
Chain Length:220
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:Q8W464 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL40
Gene (Uniprot):BOLC9T56081H
Chain IDs:UB (auth: 1i)
Chain Length:170
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A3P6DV95
Polymer Type:polypeptide(L)
Molecule:mL41
Chain IDs:VB (auth: 1j)
Chain Length:90
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL43
Chain IDs:WB (auth: 1k)
Chain Length:204
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3DUE5 Pfam ID:PF05047
Polymer Type:polypeptide(L)
Molecule:mL46
Chain IDs:XB (auth: 1l)
Chain Length:176
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:mL53
Chain IDs:YB (auth: 1m)
Chain Length:128
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:mL54
Chain IDs:ZB (auth: 1o)
Chain Length:160
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:mL59/mL64
Chain IDs:AC (auth: 1p)
Chain Length:130
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL60
Chain IDs:BC (auth: 1q)
Chain Length:78
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3BIE3
Polymer Type:polypeptide(L)
Molecule:mL80
Chain IDs:CC (auth: 1r)
Chain Length:126
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mL87
Chain IDs:DC (auth: 1s)
Chain Length:270
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3DDW7
Polymer Type:polypeptide(L)
Molecule:mL101 (rPPR4)
Chain IDs:EC (auth: 1t)
Chain Length:491
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:mL102 (rPPR5)
Chain IDs:FC (auth: 1u)
Chain Length:180
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:mL104 (rPPR9)
Chain IDs:GC (auth: 1v)
Chain Length:514
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:IC (auth: 2)
Chain Length:1766
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:A (auth: 3)
Chain Length:118
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S2
Chain IDs:B (auth: A)
Chain Length:212
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3CN01 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3m
Gene (Uniprot):rps3
Chain IDs:C (auth: B)
Chain Length:80
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A068BCX1 Pfam ID:PF00189
Polymer Type:polypeptide(L)
Molecule:uS4m
Chain IDs:D (auth: C)
Chain Length:362
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:S5 DRBM domain-containing protein
Chain IDs:E (auth: D)
Chain Length:110
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3AS28 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:bS6m
Chain IDs:F (auth: E)
Chain Length:383
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3CIR5 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS7m,Small ribosomal subunit protein uS7m
Gene (Uniprot):rps7
Chain IDs:G (auth: F)
Chain Length:410
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A068BEX5 Pfam ID:PF00177
Polymer Type:polypeptide(L)
Molecule:uS8m
Chain IDs:H (auth: G)
Chain Length:129
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:uS9m
Chain IDs:I (auth: H)
Chain Length:384
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10 domain-containing protein
Chain IDs:J (auth: I)
Chain Length:725
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3CHA1 Pfam ID:PF00338
Polymer Type:polypeptide(L)
Molecule:uS11m
Chain IDs:K (auth: J)
Chain Length:304
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:uS12m
Chain IDs:L (auth: K)
Chain Length:153
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS13m
Chain IDs:M (auth: L)
Chain Length:576
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3D1F0 Pfam ID:PF00416
Polymer Type:polypeptide(L)
Molecule:uS14m
Chain IDs:N (auth: M)
Chain Length:155
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15c
Chain IDs:O (auth: N)
Chain Length:414
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3D1Z7 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:P (auth: O)
Chain Length:136
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3ALM2 Pfam ID:PF00886
Polymer Type:polypeptide(L)
Molecule:uS17m
Chain IDs:Q (auth: P)
Chain Length:110
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:bS18m
Chain IDs:R (auth: Q)
Chain Length:237
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19m
Gene (Uniprot):RPS19
Chain IDs:S (auth: R)
Chain Length:212
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:P39697 Pfam ID:PF00076, PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S21
Chain IDs:T (auth: S)
Chain Length:100
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3AW14 Pfam ID:PF01165
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S31, mitochondrial
Chain IDs:U (auth: T)
Chain Length:94
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3C0Z4 Pfam ID:PF17067
Polymer Type:polypeptide(L)
Molecule:mS23
Chain IDs:V (auth: U)
Chain Length:192
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:mS26
Chain IDs:W (auth: V)
Chain Length:193
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein mS29
Chain IDs:X (auth: W)
Chain Length:483
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3CAV8 Pfam ID:PF10236
Polymer Type:polypeptide(L)
Molecule:mS31/mS46
Chain IDs:Y (auth: X)
Chain Length:496
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:mS33
Chain IDs:Z (auth: Y)
Chain Length:102
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:mS34
Chain IDs:AA (auth: Z)
Chain Length:153
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:mS35
Chain IDs:BA (auth: a)
Chain Length:212
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:mS37
Chain IDs:CA (auth: b)
Chain Length:80
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:mS38
Chain IDs:DA (auth: c)
Chain Length:362
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:mS41
Chain IDs:EA (auth: d)
Chain Length:110
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mS45
Chain IDs:FA (auth: e)
Chain Length:383
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A0D3BFU2 Pfam ID:PF12298
Polymer Type:polypeptide(L)
Molecule:mS47
Chain IDs:GA (auth: f)
Chain Length:410
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein mS81 (rPPR8)
Gene (Uniprot):F1N13_120
Chain IDs:HA (auth: g)
Chain Length:129
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:Q8LPF1 Pfam ID:PF01535
Polymer Type:polypeptide(L)
Molecule:mS83 (rPPR10)
Chain IDs:IA (auth: h)
Chain Length:384
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:PROP1-like PPR domain-containing protein
Gene (Uniprot):AN1_LOCUS2089
Chain IDs:JA (auth: i)
Chain Length:725
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:A0A654ECT9 Pfam ID:PF13812, PF17177
Polymer Type:polypeptide(L)
Molecule:mS76 (rPPR1)
Chain IDs:KA (auth: j)
Chain Length:304
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Polymer Type:polypeptide(L)
Molecule:mS86
Chain IDs:LA (auth: k)
Chain Length:153
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein mS80 (rPPR6)
Gene (Uniprot):F16B3.28
Chain IDs:MA (auth: l)
Chain Length:576
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis
UniProt ID:P0C896 Pfam ID:PF01535, PF13041
Ligand Molecules
ATP
K
MG
ZN
Primary Citation
Structural insights into cauliflower mitoribosome in translation state and in association with a late assembly factor.
Nat Commun 16 10839 10839 (2025)
PMID: 41330901 DOI: 10.1038/s41467-025-65864-z

Abstact

Ribosomes are key molecular machines that translate mRNA into proteins. Mitoribosomes are specific ribosomes found in mitochondria, which have been shown to be remarkably diverse across eukaryotic lineages. In plants, they possess unique features, including additional rRNA domains stabilized by plant-specific proteins. However, the structural specificities of plant mitoribosomes in translation state remained unknown. We used cryo-electron microscopy to provide a high-resolution structural characterization of the cauliflower mitoribosome, in translating and maturation states. The structure reveals the mitoribosome bound with a tRNA in the peptidyl site, along with a segment of mRNA and a nascent polypeptide. Moreover, using structural data, nanopore sequencing and mass spectrometry, we identify a set of 19 ribosomal RNA modifications. Additionally, we observe a late assembly intermediate of the small ribosomal subunit, in complex with the RsgA assembly factor. This reveals how a plant-specific extension of RsgA blocks the mRNA channel to prevent premature mRNA association before complete small subunit maturation. Our findings elucidate key aspects of translation in angiosperm plant mitochondria, revealing its distinct features compared to other eukaryotic lineages.

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Protein

Chemical

Disease

Primary Citation of related structures
9GYT
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