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:
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
Primary Citation of related structures
9GYT
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