ISDA

Deposition Date 2020-10-07

Release Date 2021-04-28

Last Version Date 2024-10-09

Entry Detail

PDB ID:

7AM2

Keywords:

RIBOSOME

Title:

Intermediate assembly of the Large subunit from Leishmania major mitochondrial ribosome

Biological Source:

Source Organism:

Leishmania tarentolae (Taxon ID: 5689)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.40 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:Ribosomal RNA
Chain IDs:VB (auth: 1)
Chain Length:16181
Number of Molecules:1
Biological Source:Leishmania tarentolae

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L3-like protein
Gene (Uniprot):LMJF_29_0030
Chain IDs:A
Chain Length:467
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:E9ADK5 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL42
Gene (Uniprot):LMJF_36_3350
Chain IDs:LA (auth: Aa)
Chain Length:195
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q183

Protein Blast

Polymer Type:polypeptide(L)
Molecule:L51_S25_CI-B8 domain-containing protein
Gene (Uniprot):LMJF_31_1550
Chain IDs:KA (auth: Ab)
Chain Length:262
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q6A7 Pfam ID:PF05047

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL49
Gene (Uniprot):LMJF_08_0560
Chain IDs:RA (auth: Ad)
Chain Length:237
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QIB3

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL53
Gene (Uniprot):LMJF_03_0150
Chain IDs:FA (auth: Ae)
Chain Length:311
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:E9ACG2

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL63
Gene (Uniprot):LMJF_05_0860
Chain IDs:GA (auth: Af)
Chain Length:155
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QJB6

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL59/64
Gene (Uniprot):LMJF_28_2360
Chain IDs:AB (auth: Ag)
Chain Length:244
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL68
Gene (Uniprot):LMJF_21_1500
Chain IDs:HA (auth: Ah)
Chain Length:570
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QC45

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL72
Gene (Uniprot):LMJF_30_2660
Chain IDs:UA (auth: Aj)
Chain Length:503
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q728

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL74
Gene (Uniprot):LMJF_36_2910
Chain IDs:JA (auth: Al)
Chain Length:346
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q1C8

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL75
Gene (Uniprot):LMJF_21_1620
Chain IDs:OA (auth: Am)
Chain Length:340
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QC22 Pfam ID:PF13041

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL76
Gene (Uniprot):LMJF_36_6050
Chain IDs:WA (auth: An)
Chain Length:331
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q0F5

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL80
Gene (Uniprot):LMJF_30_0060
Chain IDs:IA (auth: Ap)
Chain Length:240
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q7V3

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL84
Gene (Uniprot):LMJF_30_2810
Chain IDs:VA (auth: Ar)
Chain Length:205
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q712

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL85
Gene (Uniprot):LMJF_01_0060
Chain IDs:PA (auth: As)
Chain Length:249
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:E9ABZ5

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL86
Gene (Uniprot):LMJF_33_0080
Chain IDs:DA (auth: At)
Chain Length:183
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q4L5

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL87
Gene (Uniprot):LMJF_28_0730
Chain IDs:EA (auth: Au)
Chain Length:186
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q8J6

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL88
Gene (Uniprot):LMJF_07_0070
Chain IDs:YA (auth: Av)
Chain Length:192
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QIT7

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL89
Gene (Uniprot):LMJF_27_0230
Chain IDs:SA (auth: Aw)
Chain Length:187
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:E9AD00

Protein Blast

Polymer Type:polypeptide(L)
Molecule:LIM zinc-binding domain-containing protein
Gene (Uniprot):LMJF_30_0280
Chain IDs:CB (auth: Ax)
Chain Length:216
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q7T1 Pfam ID:PF00412

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL93
Gene (Uniprot):LMJF_33_0660
Chain IDs:NA (auth: Az)
Chain Length:152
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q4D9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL4m
Gene (Uniprot):LMJF_11_1360
Chain IDs:B
Chain Length:436
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QGU6 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL94
Gene (Uniprot):LMJF_04_0045
Chain IDs:T (auth: BA)
Chain Length:167
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:E9ACP5

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL95
Gene (Uniprot):LMJF_33_0690
Chain IDs:W (auth: BB)
Chain Length:156
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q4D6

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL98
Gene (Uniprot):LMJF_18_0260
Chain IDs:BA (auth: BE)
Chain Length:118
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QE16

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL99
Gene (Uniprot):LMJF_07_0420
Chain IDs:XA (auth: BF)
Chain Length:109
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QIQ1

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL100
Gene (Uniprot):CGC21_25710
Chain IDs:QA (auth: BG)
Chain Length:1347
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:A0A504WW14

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Peptidyl-prolyl cis-trans isomerase
Gene (Uniprot):CYP6
Chain IDs:TA (auth: BH)
Chain Length:229
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QBK2 Pfam ID:PF00160

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL67
Gene (Uniprot):LMJF_27_1030
Chain IDs:Y (auth: BK)
Chain Length:893
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:E9AD80

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL70
Gene (Uniprot):LMJF_30_2890
Chain IDs:ZA (auth: BM)
Chain Length:457
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q703

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL81
Gene (Uniprot):LMJF_24_0860
Chain IDs:AA (auth: BN)
Chain Length:344
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QAP7

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative ribosomal protein L14
Gene (Uniprot):LMJF_34_3815
Chain IDs:CA (auth: BO)
Chain Length:190
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q2G1 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL52,mL52
Gene (Uniprot):LMJF_13_0140
Chain IDs:MA (auth: BP)
Chain Length:254
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QGE0

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL71
Gene (Uniprot):LMJF_22_1470
Chain IDs:Z (auth: BQ)
Chain Length:445
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QBK0

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL78
Gene (Uniprot):CGC21_38360
Chain IDs:TB (auth: BR)
Chain Length:301
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:A0A504XZ90

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNAj-like protein
Gene (Uniprot):LMJF_30_1030
Chain IDs:DB (auth: BS)
Chain Length:416
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q7K0 Pfam ID:PF00226

Protein Blast

Polymer Type:polypeptide(L)
Molecule:G domain-containing protein
Gene (Uniprot):LMJF_35_5210
Chain IDs:JB (auth: BT)
Chain Length:464
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:E9AFZ4 Pfam ID:PF01926

Protein Blast

Polymer Type:polypeptide(L)
Molecule:GTPase Der
Gene (Uniprot):LMJF_26_0270
Chain IDs:KB (auth: BU)
Chain Length:497
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q9G4 Pfam ID:PF01926, PF14714

Protein Blast

Polymer Type:polypeptide(L)
Molecule:G domain-containing protein
Gene (Uniprot):LMJF_32_3020
Chain IDs:MB (auth: BV)
Chain Length:787
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q4X0 Pfam ID:PF01926

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DEAD/DEAH box helicase-like protein
Gene (Uniprot):LMJF_09_0830
Chain IDs:LB (auth: BW)
Chain Length:776
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QHU1 Pfam ID:PF00270, PF00271

Protein Blast

Polymer Type:polypeptide(L)
Molecule:SpoU_methylase domain-containing protein
Gene (Uniprot):LMJF_35_2890
Chain IDs:EB (auth: BY), FB (auth: BX)
Chain Length:569
Number of Molecules:2
Biological Source:Leishmania tarentolae

UniProt ID:E9AFB3 Pfam ID:PF00588

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pseudouridylate synthase-like protein
Gene (Uniprot):LMJF_01_0280
Chain IDs:GB (auth: BZ)
Chain Length:413
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:E9AC17 Pfam ID:PF00849

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Peptidyl-prolyl cis-trans isomerase
Gene (Uniprot):CYP10
Chain IDs:BB (auth: Bl)
Chain Length:266
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q1A6 Pfam ID:PF00160

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL_L9 domain-containing protein
Gene (Uniprot):LMJF_08_0240
Chain IDs:C
Chain Length:262
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QIE5 Pfam ID:PF01281

Protein Blast

Polymer Type:polypeptide(L)
Molecule:TRUD domain-containing protein
Gene (Uniprot):LMJF_11_1370
Chain IDs:U (auth: CA)
Chain Length:618
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QGU5

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA uridylyltransferase
Gene (Uniprot):L5213T.03
Chain IDs:X (auth: CB)
Chain Length:202
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q9NE59 Pfam ID:PF02410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein
Gene (Uniprot):ACP
Chain IDs:HB (auth: CC)
Chain Length:150
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:E9AD06 Pfam ID:PF00550

Protein Blast

Polymer Type:polypeptide(L)
Molecule:L0R8F8
Gene (Uniprot):LMJF_14_0580
Chain IDs:IB (auth: CD)
Chain Length:126
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QFS7

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative ribosomal protein L11
Gene (Uniprot):LMJF_27_2220
Chain IDs:D (auth: E)
Chain Length:346
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:E9ACT9 Pfam ID:PF03946, PF00298

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13-like protein
Gene (Uniprot):LMJF_34_3680
Chain IDs:E (auth: F)
Chain Length:171
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q2H6 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal_L18e/L15P domain-containing protein
Gene (Uniprot):LMJF_16_0010
Chain IDs:F (auth: G)
Chain Length:374
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QF19 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative 50S ribosomal protein L17
Gene (Uniprot):LMJF_16_0160
Chain IDs:G (auth: I)
Chain Length:305
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QF04 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL19m
Gene (Uniprot):LMJF_20_0530
Chain IDs:H (auth: J)
Chain Length:144
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QCY7

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL20m
Gene (Uniprot):LMJF_36_3260
Chain IDs:I (auth: K)
Chain Length:194
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q192

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL21m
Gene (Uniprot):LMJF_14_0780
Chain IDs:J (auth: L)
Chain Length:186
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QFQ5 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL22m
Gene (Uniprot):LMJF_22_0870
Chain IDs:K (auth: M)
Chain Length:279
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QBR0 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL23m
Gene (Uniprot):LMJF_25_0890
Chain IDs:L (auth: N)
Chain Length:252
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QA05

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL24m
Gene (Uniprot):LMJF_25_1640
Chain IDs:M (auth: O)
Chain Length:476
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q9S7

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL28m
Gene (Uniprot):LMJF_30_2750
Chain IDs:N (auth: Q)
Chain Length:234
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL29m
Gene (Uniprot):LMJF_04_0270
Chain IDs:O (auth: R)
Chain Length:480
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q9XZY7 Pfam ID:PF06984

Polymer Type:polyribonucleotide
Molecule:R1
Chain IDs:WB (auth: R1)
Chain Length:3
Number of Molecules:1
Biological Source:Leishmania tarentolae

Polymer Type:polyribonucleotide
Molecule:R2
Chain IDs:XB (auth: R2)
Chain Length:35
Number of Molecules:1
Biological Source:Leishmania tarentolae

Polymer Type:polyribonucleotide
Molecule:R5
Chain IDs:YB (auth: R5)
Chain Length:5
Number of Molecules:1
Biological Source:Leishmania tarentolae

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL30m
Gene (Uniprot):LMJF_04_0860
Chain IDs:P (auth: S)
Chain Length:409
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q9U0Z7

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL32m
Gene (Uniprot):LMJF_34_2310
Chain IDs:Q (auth: T)
Chain Length:83
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q2W9

Polymer Type:polypeptide(L)
Molecule:U1
Chain IDs:PB (auth: U1)
Chain Length:46
Number of Molecules:1
Biological Source:Leishmania tarentolae

Polymer Type:polypeptide(L)
Molecule:U2
Chain IDs:UB (auth: U2)
Chain Length:37
Number of Molecules:1
Biological Source:Leishmania tarentolae

Polymer Type:polypeptide(L)
Molecule:U3
Chain IDs:QB (auth: U3)
Chain Length:75
Number of Molecules:1
Biological Source:Leishmania tarentolae

Polymer Type:polypeptide(L)
Molecule:U4
Chain IDs:RB (auth: U4)
Chain Length:136
Number of Molecules:1
Biological Source:Leishmania tarentolae

Polymer Type:polypeptide(L)
Molecule:U5
Chain IDs:SB (auth: U5)
Chain Length:94
Number of Molecules:1
Biological Source:Leishmania tarentolae

Polymer Type:polypeptide(L)
Molecule:U6
Chain IDs:OB (auth: U6)
Chain Length:187
Number of Molecules:1
Biological Source:Leishmania tarentolae

Polymer Type:polypeptide(L)
Molecule:mL78
Chain IDs:NB (auth: U7)
Chain Length:40
Number of Molecules:1
Biological Source:Leishmania tarentolae

Polymer Type:polypeptide(L)
Molecule:U8
Chain IDs:ZB (auth: U8)
Chain Length:59
Number of Molecules:1
Biological Source:Leishmania tarentolae

Polymer Type:polypeptide(L)
Molecule:UA
Chain IDs:V (auth: UA)
Chain Length:203
Number of Molecules:1
Biological Source:Leishmania tarentolae

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bL35m
Gene (Uniprot):LMJF_21_0100
Chain IDs:R (auth: V)
Chain Length:151
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4QCK6

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL41
Gene (Uniprot):LMJF_36_3653
Chain IDs:S (auth: Z)
Chain Length:197
Number of Molecules:1
Biological Source:Leishmania tarentolae

UniProt ID:Q4Q152

Ligand Molecules

ATP

GTP

Primary Citation

Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis.

Soufari, H, Waltz, F, Parrot, C, Durrieu-Gaillard, S, Bochler, A, Kuhn, L, Sissler, M, Hashem, Y.Show

Proc.Natl.Acad.Sci.USA 117 29851 29861 (2020)

PMID: 33168716 DOI: 10.1073/pnas.2011301117

Abstact

Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential for the parasite survival. In kinetoplastid mitochondria, most of the molecular machineries and gene expression processes have significantly diverged and specialized, with an extreme example being their mitochondrial ribosomes. These large complexes are in charge of translating the few essential mRNAs encoded by mitochondrial genomes. Structural studies performed in Trypanosoma brucei already highlighted the numerous peculiarities of these mitoribosomes and the maturation of their small subunit. However, several important aspects mainly related to the large subunit (LSU) remain elusive, such as the structure and maturation of its ribosomal RNA. Here we present a cryo-electron microscopy study of the protozoans Leishmania tarentolae and Trypanosoma cruzi mitoribosomes. For both species, we obtained the structure of their mature mitoribosomes, complete rRNA of the LSU, as well as previously unidentified ribosomal proteins. In addition, we introduce the structure of an LSU assembly intermediate in the presence of 16 identified maturation factors. These maturation factors act on both the intersubunit and the solvent sides of the LSU, where they refold and chemically modify the rRNA and prevent early translation before full maturation of the LSU.

Legend

Protein

Chemical

Disease

Primary Citation of related structures