7AM2

Intermediate assembly of the Large subunit from Leishmania major mitochondrial ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

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.

(2020) Proc Natl Acad Sci U S A 117: 29851-29861

  • DOI: https://doi.org/10.1073/pnas.2011301117
  • Primary Citation of Related Structures:  
    7AIH, 7AM2, 7ANE, 7AOR

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Institut Européen de Chimie et Biologie, U1212 INSERM, UMR5320 CNRS, Université de Bordeaux, F-33600 Pessac, France.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3-like protein467Leishmania tarentolaeMutation(s): 0 
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Find proteins for E9ADK5 (Leishmania major)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uL4m436Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4QGU6 (Leishmania major)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL_L9 domain-containing protein262Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4QIE5 (Leishmania major)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L11D [auth E]346Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for E9ACT9 (Leishmania major)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13-like proteinE [auth F]171Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L18e/L15P domain-containing proteinF [auth G]374Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 50S ribosomal protein L17G [auth I]305Leishmania tarentolaeMutation(s): 0 
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Find proteins for Q4QF04 (Leishmania major)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
bL19mH [auth J]144Leishmania tarentolaeMutation(s): 0 
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Find proteins for Q4QCY7 (Leishmania major)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
bL20mI [auth K]194Leishmania tarentolaeMutation(s): 0 
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Find proteins for Q4Q192 (Leishmania major)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
bL21mJ [auth L]186Leishmania tarentolaeMutation(s): 0 
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Find proteins for Q4QFQ5 (Leishmania major)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
uL22mK [auth M]279Leishmania tarentolaeMutation(s): 0 
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Find proteins for Q4QBR0 (Leishmania major)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
uL23mL [auth N]252Leishmania tarentolaeMutation(s): 0 
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Find proteins for Q4QA05 (Leishmania major)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
uL24mM [auth O]476Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4Q9S7 (Leishmania major)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
bL28mN [auth Q]234Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4Q719 (Leishmania major)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uL29mO [auth R]480Leishmania tarentolaeMutation(s): 0 
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Find proteins for Q9XZY7 (Leishmania major)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
uL30mP [auth S]409Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q9U0Z7 (Leishmania major)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
bL32mQ [auth T]83Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4Q2W9 (Leishmania major)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
bL35mR [auth V]151Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4QCK6 (Leishmania major)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
mL41S [auth Z]197Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4Q152 (Leishmania major)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
mL94T [auth BA]167Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for E9ACP5 (Leishmania major)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
TRUD domain-containing proteinU [auth CA]618Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4QGU5 (Leishmania major)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
UAV [auth UA]203Leishmania tarentolaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
mL95W [auth BB]156Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4Q4D6 (Leishmania major)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RNA uridylyltransferaseX [auth CB]202Leishmania tarentolaeMutation(s): 0 
EC: 2.7.7.52
UniProt
Find proteins for Q9NE59 (Leishmania major)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
mL67Y [auth BK]893Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for E9AD80 (Leishmania major)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
mL71Z [auth BQ]445Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4QBK0 (Leishmania major)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
mL81AA [auth BN]344Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4QAP7 (Leishmania major)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
mL98BA [auth BE]118Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4QE16 (Leishmania major)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L14CA [auth BO]190Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4Q2G1 (Leishmania major)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
mL86DA [auth At]183Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
mL87EA [auth Au]186Leishmania tarentolaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
mL53FA [auth Ae]311Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for E9ACG2 (Leishmania major)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
mL63GA [auth Af]155Leishmania tarentolaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
mL68HA [auth Ah]570Leishmania tarentolaeMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
mL80IA [auth Ap]240Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4Q7V3 (Leishmania major)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
mL74JA [auth Al]346Leishmania tarentolaeMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
L51_S25_CI-B8 domain-containing proteinKA [auth Ab]262Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
mL42LA [auth Aa]195Leishmania tarentolaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
mL52,mL52MA [auth BP]254Leishmania tarentolaeMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
mL93NA [auth Az]152Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4Q4D9 (Leishmania major)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
mL75OA [auth Am]340Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
mL85PA [auth As]249Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
mL100QA [auth BG]1,347Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A504WW14 (Leishmania donovani)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
mL49RA [auth Ad]237Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4QIB3 (Leishmania major)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
mL89SA [auth Aw]187Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for E9AD00 (Leishmania major)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseTA [auth BH]229Leishmania tarentolaeMutation(s): 0 
EC: 5.2.1.8
UniProt
Find proteins for Q4QBK2 (Leishmania major)
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UniProt GroupQ4QBK2
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
mL72UA [auth Aj]503Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
mL84VA [auth Ar]205Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
mL76WA [auth An]331Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
mL99XA [auth BF]109Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
mL88YA [auth Av]192Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
mL70ZA [auth BM]457Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
mL59/64AB [auth Ag]244Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseBB [auth Bl]266Leishmania tarentolaeMutation(s): 0 
EC: 5.2.1.8
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
LIM zinc-binding domain-containing proteinCB [auth Ax]216Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
DNAj-like proteinDB [auth BS]416Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
SpoU_methylase domain-containing proteinEB [auth BY],
FB [auth BX]
569Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Pseudouridylate synthase-like proteinGB [auth BZ]413Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinHB [auth CC]150Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
L0R8F8IB [auth CD]126Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
G domain-containing proteinJB [auth BT]464Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase DerKB [auth BU]497Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
DEAD/DEAH box helicase-like proteinLB [auth BW]776Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
G domain-containing proteinMB [auth BV]787Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
mL78NB [auth U7]40Leishmania tarentolaeMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
U6OB [auth U6]187Leishmania tarentolaeMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
U1PB [auth U1]46Leishmania tarentolaeMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
U3QB [auth U3]75Leishmania tarentolaeMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
U4RB [auth U4]136Leishmania tarentolaeMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
U5SB [auth U5]94Leishmania tarentolaeMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
mL78TB [auth BR]301Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A504XZ90 (Leishmania donovani)
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
U2UB [auth U2]37Leishmania tarentolaeMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
U8ZB [auth U8]59Leishmania tarentolaeMutation(s): 0 
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Entity ID: 73
MoleculeChains LengthOrganismImage
Ribosomal RNAVB [auth 1]19,000Leishmania tarentolae
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Entity ID: 74
MoleculeChains LengthOrganismImage
R1WB [auth R1]3Leishmania tarentolae
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Entity ID: 75
MoleculeChains LengthOrganismImage
R2XB [auth R2]35Leishmania tarentolae
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Entity ID: 76
MoleculeChains LengthOrganismImage
R5YB [auth R5]5Leishmania tarentolae
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)France--

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release