ISDA: 9EVS

Deposition Date 2024-04-02

Release Date 2025-09-03

Last Version Date 2025-12-17

Entry Detail

PDB ID:

9EVS

Keywords:

RIBOSOME

Title:

Structure of the flowering plant mitoribosome with P-site tRNA

Biological Source:

Source Organism:

Brassica oleracea var. botrytis (Taxon ID: 3715)
Brassica oleracea var. oleracea (Taxon ID: 109376)
Arabidopsis thaliana (Taxon ID: 3702)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.05 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:26S rRNA
Chain IDs:Z (auth: 1)
Chain Length:2922
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL2m C-ter
Chain IDs:BA (auth: 1B)
Chain Length:220
Number of Molecules:1
Biological Source:Brassica oleracea var. oleracea

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2mz, N-terminal part
Gene (Uniprot):RPL2-N
Chain IDs:CA (auth: 1C)
Chain Length:135
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:P93311 Pfam ID:PF00181

Polymer Type:polypeptide(L)
Molecule:uL3m
Chain IDs:DA (auth: 1D)
Chain Length:319
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL4m
Chain IDs:EA (auth: 1E)
Chain Length:297
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL5m
Chain IDs:FA (auth: 1F)
Chain Length:146
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL6m
Chain IDs:GA (auth: 1G)
Chain Length:162
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL9m
Chain IDs:HA (auth: 1H)
Chain Length:219
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL10m
Chain IDs:IA (auth: 1I)
Chain Length:247
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL11m
Chain IDs:JA (auth: 1J)
Chain Length:156
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL13m
Chain IDs:KA (auth: 1K)
Chain Length:204
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL14m
Chain IDs:LA (auth: 1L)
Chain Length:233
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL15m
Chain IDs:MA (auth: 1M)
Chain Length:128
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL16m
Chain IDs:NA (auth: 1N)
Chain Length:179
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL17m
Chain IDs:OA (auth: 1O)
Chain Length:125
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL18m
Chain IDs:PA (auth: 1P)
Chain Length:130
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL19m
Chain IDs:QA (auth: 1Q)
Chain Length:79
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL20m
Chain IDs:RA (auth: 1R)
Chain Length:167
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL21m
Chain IDs:SA (auth: 1S)
Chain Length:270
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL22m
Chain IDs:TA (auth: 1T)
Chain Length:264
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL23m
Chain IDs:UA (auth: 1U)
Chain Length:757
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL24m
Chain IDs:VA (auth: 1V)
Chain Length:521
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL25-2m
Chain IDs:WA (auth: 1W)
Chain Length:249
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL25m
Chain IDs:XA (auth: 1X)
Chain Length:4
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL27m
Chain IDs:YA (auth: 1Y)
Chain Length:156
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL28m
Chain IDs:ZA (auth: 1Z)
Chain Length:212
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL29m
Chain IDs:AB (auth: 1a)
Chain Length:144
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uL30m
Chain IDs:BB (auth: 1b)
Chain Length:220
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL31m
Chain IDs:CB (auth: 1c)
Chain Length:135
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL32m
Chain IDs:DB (auth: 1d)
Chain Length:319
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL33m
Chain IDs:EB (auth: 1e)
Chain Length:297
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL34m
Chain IDs:FB (auth: 1f)
Chain Length:146
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL35m
Chain IDs:GB (auth: 1g)
Chain Length:162
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bL36m
Chain IDs:HB (auth: 1h)
Chain Length:219
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mL40
Chain IDs:IB (auth: 1i)
Chain Length:247
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mL41
Chain IDs:JB (auth: 1j)
Chain Length:156
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mL43
Chain IDs:KB (auth: 1k)
Chain Length:204
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mL46
Chain IDs:LB (auth: 1l)
Chain Length:233
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mL53
Chain IDs:MB (auth: 1m)
Chain Length:128
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mL54
Chain IDs:NB (auth: 1o)
Chain Length:125
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mL59/mL64
Chain IDs:OB (auth: 1p)
Chain Length:130
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mL60
Chain IDs:PB (auth: 1q)
Chain Length:79
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mL80
Chain IDs:QB (auth: 1r)
Chain Length:167
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mL87
Chain IDs:RB (auth: 1s)
Chain Length:270
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mL101 (rPPR4)
Chain IDs:SB (auth: 1t)
Chain Length:264
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mL102 (rPPR5)
Chain IDs:TB (auth: 1u)
Chain Length:757
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mL104 (rPPR9)
Chain IDs:UB (auth: 1v)
Chain Length:521
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:Nascent peptide
Chain IDs:VB (auth: 1x)
Chain Length:4
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:XB (auth: 2)
Chain Length:1591
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:AA (auth: 3)
Chain Length:118
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:WB (auth: 5)
Chain Length:76
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:YB (auth: 6)
Chain Length:6
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uS2m
Chain IDs:JC (auth: A)
Chain Length:424
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 uS3m
Gene (Uniprot):rps3
Chain IDs:A (auth: B)
Chain Length:554
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

UniProt ID:A0A068BCX1 Pfam ID:PF00189

Polymer Type:polypeptide(L)
Molecule:uS4m
Chain IDs:B (auth: C)
Chain Length:128
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uS5m
Chain IDs:C (auth: D)
Chain Length:501
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bS6m
Chain IDs:D (auth: E)
Chain Length:138
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS7m,Small ribosomal subunit protein uS7m
Gene (Uniprot):rps7
Chain IDs:E (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:F (auth: G)
Chain Length:129
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uS9m
Chain IDs:G (auth: H)
Chain Length:384
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uS10m
Chain IDs:H (auth: I)
Chain Length:725
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uS11m
Chain IDs:I (auth: J)
Chain Length:408
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uS12m
Chain IDs:J (auth: K)
Chain Length:155
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uS13m
Chain IDs:K (auth: L)
Chain Length:154
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uS14m
Chain IDs:L (auth: M)
Chain Length:155
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uS15m
Chain IDs:M (auth: N)
Chain Length:414
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bS16m
Chain IDs:N (auth: O)
Chain Length:136
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uS17m
Chain IDs:O (auth: P)
Chain Length:110
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bS18m
Chain IDs:P (auth: Q)
Chain Length:237
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:uS19m
Chain IDs:Q (auth: R)
Chain Length:212
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bS21m
Chain IDs:R (auth: S)
Chain Length:100
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:bTHXm
Chain IDs:S (auth: T)
Chain Length:94
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mS23
Chain IDs:T (auth: U)
Chain Length:192
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mS26
Chain IDs:U (auth: V)
Chain Length:193
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mS29
Chain IDs:V (auth: W)
Chain Length:483
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mS31/mS46
Chain IDs:W (auth: X)
Chain Length:496
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mS33
Chain IDs:X (auth: Y)
Chain Length:102
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mS34
Chain IDs:Y (auth: Z)
Chain Length:153
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mS35
Chain IDs:ZB (auth: a)
Chain Length:424
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mS37
Chain IDs:AC (auth: b)
Chain Length:554
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mS38
Chain IDs:BC (auth: c)
Chain Length:128
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mS41
Chain IDs:CC (auth: d)
Chain Length:501
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:DC (auth: e)
Chain Length:138
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

UniProt ID:A0A0D3BFU2 Pfam ID:PF12298

Polymer Type:polypeptide(L)
Molecule:mS47
Chain IDs:EC (auth: f)
Chain Length:410
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mS83 (rPPR10)
Chain IDs:FC (auth: h)
Chain Length:384
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mS77 (NFD5)
Chain IDs:GC (auth: i)
Chain Length:725
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mS76 (rPPR1)
Chain IDs:HC (auth: j)
Chain Length:408
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Polymer Type:polypeptide(L)
Molecule:mS86
Chain IDs:IC (auth: k)
Chain Length:155
Number of Molecules:1
Biological Source:Brassica oleracea var. botrytis

Ligand Molecules

ATP

CLM

Primary Citation

Structural insights into cauliflower mitoribosome in translation state and in association with a late assembly factor.

Skaltsogiannis, V, Wolff, P, Nguyen, T.T, Corre, N, Pflieger, D, Blevins, T, Hashem, Y, Giege, P, Waltz, F.Show

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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