7AOI image
Entry Detail
PDB ID:
7AOI
EMDB ID:
Keywords:
Title:
Trypanosoma brucei mitochondrial ribosome large subunit assembly intermediate
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2020-10-14
Release Date:
2020-12-02
Method Details:
Experimental Method:
Resolution:
3.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:bL28m
Chain IDs:A (auth: A1)
Chain Length:217
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:uL29m
Chain IDs:B (auth: A2)
Chain Length:463
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:uL30m
Chain IDs:C (auth: A3)
Chain Length:150
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:bL32m
Chain IDs:D (auth: A5)
Chain Length:55
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:bL33m
Chain IDs:E (auth: A8)
Chain Length:142
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polyribonucleotide
Description:mt-LSU rRNA
Chain IDs:F (auth: AA)
Chain Length:758
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Ribosomal protein L3 mitochondrial, putative
Chain IDs:G (auth: AE)
Chain Length:367
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Ribosomal protein L4/L1 family
Chain IDs:H (auth: AF)
Chain Length:133
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:RIBOSOMAL_L9 domain-containing protein
Chain IDs:I (auth: AI)
Chain Length:212
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Ribosomal protein L11,uL11m
Chain IDs:J (auth: AK)
Chain Length:278
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:K (auth: AN)
Chain Length:171
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Ribosomal_L18e/L15P domain-containing protein
Chain IDs:L (auth: AP)
Chain Length:288
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:M (auth: AR)
Chain Length:256
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:bL19m
Chain IDs:N (auth: AT)
Chain Length:145
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:bL20m
Chain IDs:O (auth: AU)
Chain Length:196
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Ribosomal protein L21
Chain IDs:P (auth: AV)
Chain Length:197
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Ribosomal protein L22p/L17e
Chain IDs:Q (auth: AW)
Chain Length:277
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Ribosomal protein L23
Chain IDs:R (auth: AX)
Chain Length:165
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:uL24m
Chain IDs:S (auth: AY)
Chain Length:340
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL41
Chain IDs:T (auth: Ae)
Chain Length:367
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL42
Chain IDs:U (auth: Af)
Chain Length:133
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain containing protein
Chain IDs:V (auth: Ag)
Chain Length:185
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL49
Chain IDs:W (auth: Al)
Chain Length:182
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL52
Chain IDs:X (auth: Ao)
Chain Length:133
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL53
Chain IDs:Y (auth: Ap)
Chain Length:288
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL63
Chain IDs:Z (auth: At)
Chain Length:145
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL64,mL64
Chain IDs:AA (auth: Av)
Chain Length:197
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL67
Chain IDs:BA
Chain Length:798
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL68,mL68,mL68
Chain IDs:CA (auth: BB)
Chain Length:371
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL70
Chain IDs:DA (auth: BD)
Chain Length:417
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL71
Chain IDs:EA (auth: BE)
Chain Length:438
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Tetratricopeptide repeat
Chain IDs:FA (auth: BF)
Chain Length:421
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL74
Chain IDs:GA (auth: BH)
Chain Length:92
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Mitochondrial RNA binding complex 1 subunit
Chain IDs:HA (auth: BI)
Chain Length:323
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL76
Chain IDs:IA (auth: BJ)
Chain Length:161
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Chaperone protein DNAj, putative,mL77,Chaperone protein DNAj, putative
Chain IDs:JA (auth: BK)
Chain Length:273
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL78
Chain IDs:KA (auth: BL)
Chain Length:276
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL80
Chain IDs:LA (auth: BN)
Chain Length:214
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL81
Chain IDs:MA (auth: BO)
Chain Length:227
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Peptidyl-prolyl cis-trans isomerase
Chain IDs:NA (auth: BQ)
Chain Length:185
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL84
Chain IDs:OA (auth: BR)
Chain Length:195
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL85
Chain IDs:PA (auth: BS)
Chain Length:144
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL86
Chain IDs:QA (auth: BT)
Chain Length:167
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL87
Chain IDs:RA (auth: BU)
Chain Length:82
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL89
Chain IDs:SA (auth: BW)
Chain Length:187
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:LIM domain containing protein,mL90
Chain IDs:TA (auth: BX)
Chain Length:116
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Peptidyl-prolyl cis-trans isomerase
Chain IDs:UA (auth: BZ)
Chain Length:189
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL93
Chain IDs:VA (auth: Ba)
Chain Length:798
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL94
Chain IDs:WA (auth: Bb)
Chain Length:371
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL95
Chain IDs:XA (auth: Bc)
Chain Length:137
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL98
Chain IDs:YA (auth: Bf)
Chain Length:421
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL99
Chain IDs:ZA (auth: Bg)
Chain Length:82
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL100,mL100
Chain IDs:AB (auth: Bh)
Chain Length:92
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:UNK1
Chain IDs:BB (auth: UA)
Chain Length:46
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:UNK2
Chain IDs:CB (auth: UB)
Chain Length:9
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:UNK3
Chain IDs:DB (auth: UC)
Chain Length:14
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:UNK4
Chain IDs:EB (auth: UD)
Chain Length:8
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:UNK5
Chain IDs:FB (auth: UE)
Chain Length:12
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:UNK6/mt-LAF15_2
Chain IDs:GB (auth: UF)
Chain Length:139
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:UNK7
Chain IDs:HB (auth: UG)
Chain Length:19
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:UNK8
Chain IDs:IB (auth: UH)
Chain Length:17
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:UNK9
Chain IDs:JB (auth: UI)
Chain Length:39
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:UNK10
Chain IDs:KB (auth: UJ)
Chain Length:25
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:UNK11
Chain IDs:LB (auth: UK)
Chain Length:47
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mt-LAF7,mt-LAF7
Chain IDs:MB (auth: XA)
Chain Length:155
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:DEAD-box helicase, putative,mt-LAF2
Chain IDs:NB (auth: XB)
Chain Length:668
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mt-LAF4
Chain IDs:OB (auth: XC)
Chain Length:616
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Acyl carrier protein
Chain IDs:PB (auth: XD), QB (auth: XE)
Chain Length:83
Number of Molecules:2
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mt-LAF15_1
Chain IDs:RB (auth: XF)
Chain Length:198
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:SB (auth: XG)
Chain Length:170
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mt-LAF8
Chain IDs:TB (auth: XH)
Chain Length:533
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mt-LAF14
Chain IDs:UB (auth: XI)
Chain Length:703
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:RNA uridylyltransferase
Chain IDs:VB (auth: XJ)
Chain Length:150
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:GTP-binding protein, putative,mt-EngA
Chain IDs:WB (auth: XL)
Chain Length:528
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Complex1-LYR-like
Chain IDs:XB (auth: XM)
Chain Length:91
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mt-LAF12
Chain IDs:YB (auth: XN)
Chain Length:620
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:SpoU rRNA Methylase family
Chain IDs:ZB (auth: XO)
Chain Length:428
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Pseudouridylate synthase, putative
Chain IDs:AC (auth: XP)
Chain Length:371
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:GTP-binding protein
Chain IDs:BC (auth: XQ)
Chain Length:305
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:Lipase (Class 3)
Chain IDs:CC (auth: XR)
Chain Length:161
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mL101
Chain IDs:DC (auth: XS)
Chain Length:182
Number of Molecules:1
Biological Source:Trypanosoma brucei
Polymer Type:polypeptide(L)
Description:mt-LAF19
Chain IDs:EC (auth: XT)
Chain Length:97
Number of Molecules:1
Biological Source:Trypanosoma brucei
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
4HH PB SER modified residue
Primary Citation
Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit.
Embo J. 40 e106292 e106292 (2021)
PMID: 33576519 DOI: 10.15252/embj.2020106292

Abstact

Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased protein mass to provide insights into the biogenesis of the mitoribosomal large subunit. Structural characterization of a stable assembly intermediate revealed 22 assembly factors, some of which have orthologues/counterparts/homologues in mammalian genomes. These assembly factors form a protein network that spans a distance of 180 Å, shielding the ribosomal RNA surface. The central protuberance and L7/L12 stalk are not assembled entirely and require removal of assembly factors and remodeling of the mitoribosomal proteins to become functional. The conserved proteins GTPBP7 and mt-EngA are bound together at the subunit interface in proximity to the peptidyl transferase center. A mitochondrial acyl-carrier protein plays a role in docking the L1 stalk, which needs to be repositioned during maturation. Additional enzymatically deactivated factors scaffold the assembly while the exit tunnel is blocked. Together, this extensive network of accessory factors stabilizes the immature sites and connects the functionally important regions of the mitoribosomal large subunit.

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Protein

Chemical

Disease

Primary Citation of related structures