7AIH

The Large subunit of the Kinetoplastid mitochondrial ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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: 10.1073/pnas.2011301117
  • Primary Citation of Related Structures:  
    7AIH, 7AM2, 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 ...

    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; m.sissler@iecb.u-bordeaux.fr yaser.hashem@inserm.fr.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L3-like proteinA467Leishmania majorMutation(s): 0 
Gene Names: LMJF_29_0030
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
uL4mB436Leishmania majorMutation(s): 0 
Gene Names: LMJF_11_1360
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL_L9 domain-containing proteinC262Leishmania majorMutation(s): 0 
Gene Names: LMJF_08_0240
Find proteins for Q4QIE5 (Leishmania major)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
uL10mD204Leishmania majorMutation(s): 0 
Gene Names: LMJF_08_0920
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Putative ribosomal protein L11E346Leishmania majorMutation(s): 0 
Gene Names: LMJF_27_2220
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13-like proteinF171Leishmania majorMutation(s): 0 
Gene Names: LMJF_34_3680
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal_L18e/L15P domain-containing proteinG374Leishmania majorMutation(s): 0 
Gene Names: LMJF_16_0010
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal_L16 domain-containing proteinH168Leishmania majorMutation(s): 0 
Gene Names: LMJF_14_0950
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Putative 50S ribosomal protein L17I305Leishmania majorMutation(s): 0 
Gene Names: LMJF_16_0160
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
bL19mJ144Leishmania majorMutation(s): 0 
Gene Names: LMJF_20_0530
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
bL20K194Leishmania majorMutation(s): 0 
Gene Names: LMJF_36_3260
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
bL21mL186Leishmania majorMutation(s): 0 
Gene Names: LMJF_14_0780
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
uL22mM279Leishmania majorMutation(s): 0 
Gene Names: LMJF_22_0870
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
uL23mN252Leishmania majorMutation(s): 0 
Gene Names: LMJF_25_0890
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
uL24mO476Leishmania majorMutation(s): 0 
Gene Names: LMJF_25_1640
Find proteins for Q4Q9S7 (Leishmania major)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
bL27mP185Leishmania majorMutation(s): 0 
Gene Names: LMJF_13_1200
Find proteins for Q4QG34 (Leishmania major)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
bL28mQ234Leishmania majorMutation(s): 0 
Gene Names: LMJF_30_2750
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
uL29mR480Leishmania majorMutation(s): 0 
Gene Names: LMJF_04_0270
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
uL30mS409Leishmania majorMutation(s): 0 
Gene Names: LMJF_04_0860
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
bL32mT83Leishmania majorMutation(s): 0 
Gene Names: LMJF_34_2310
Find proteins for Q4Q2W9 (Leishmania major)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
bL33mU118Leishmania majorMutation(s): 0 
Gene Names: LMJF_34_2860
Find proteins for Q4Q2Q8 (Leishmania major)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
bL35mV151Leishmania majorMutation(s): 0 
Gene Names: LMJF_21_0100
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
bL36mW186Leishmania majorMutation(s): 0 
Gene Names: LMJF_31_1590
Find proteins for Q4Q6A3 (Leishmania major)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
mL38X513Leishmania majorMutation(s): 0 
Gene Names: LMJF_32_1770
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
mL40Y292Leishmania majorMutation(s): 0 
Gene Names: LMJF_33_1390
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
mL41Z197Leishmania majorMutation(s): 0 
Gene Names: LMJF_36_3653
Find proteins for Q4Q152 (Leishmania major)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
mL94AA [auth BA]167Leishmania majorMutation(s): 0 
Gene Names: LMJF_04_0045
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
UABA [auth UA]203Leishmania majorMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
mL95CA [auth BB]156Leishmania majorMutation(s): 0 
Gene Names: LMJF_33_0690
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
mL89DA [auth Aw]187Leishmania majorMutation(s): 0 
Gene Names: LMJF_27_0230
Find proteins for E9AD00 (Leishmania major)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
bL31mEA [auth Bj]185Leishmania majorMutation(s): 0 
Gene Names: LMJF_36_6190
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
mL76FA [auth An]331Leishmania majorMutation(s): 0 
Gene Names: LMJF_36_6050
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
mL74GA [auth Al]346Leishmania majorMutation(s): 0 
Gene Names: LMJF_36_2910
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseHA [auth BI]266Leishmania majorMutation(s): 0 
Gene Names: CYP10LMJF_36_3130
EC: 5.2.1.8
Find proteins for Q4Q1A6 (Leishmania major)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
mL93IA [auth Az]152Leishmania majorMutation(s): 0 
Gene Names: LMJF_33_0660
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
mL86JA [auth At]183Leishmania majorMutation(s): 0 
Gene Names: LMJF_33_0080
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
mL96KA [auth BC]147Leishmania majorMutation(s): 0 
Gene Names: LMJF_32_1440
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
L51_S25_CI-B8 domain-containing proteinLA [auth Ab]262Leishmania majorMutation(s): 0 
Gene Names: LMJF_31_1550
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
mL69MA [auth Ai]479Leishmania majorMutation(s): 0 
Gene Names: LMJF_30_0580
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
mL80NA [auth Ap]240Leishmania majorMutation(s): 0 
Gene Names: LMJF_30_0060
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
mL87OA [auth Au]186Leishmania majorMutation(s): 0 
Gene Names: LMJF_28_0730
Find proteins for Q4Q8J6 (Leishmania major)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
mL42PA [auth Aa]195Leishmania majorMutation(s): 0 
Gene Names: LMJF_36_3350
Find proteins for Q4Q183 (Leishmania major)
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
mL79QA [auth Ao]284Leishmania majorMutation(s): 0 
Gene Names: LMJF_32_2280
Find proteins for Q4Q547 (Leishmania major)
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
mL70RA [auth BM]457Leishmania majorMutation(s): 0 
Gene Names: LMJF_30_2890
Find proteins for Q4Q703 (Leishmania major)
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
mL84SA [auth Ar]205Leishmania majorMutation(s): 0 
Gene Names: LMJF_30_2810
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
mL72TA [auth Aj]503Leishmania majorMutation(s): 0 
Gene Names: LMJF_30_2660
Find proteins for Q4Q728 (Leishmania major)
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseUA [auth BH]229Leishmania majorMutation(s): 0 
Gene Names: CYP6LMJF_22_1450
EC: 5.2.1.8
Find proteins for Q4QBK2 (Leishmania major)
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
mL75VA [auth Am]340Leishmania majorMutation(s): 0 
Gene Names: LMJF_21_1620
Find proteins for Q4QC22 (Leishmania major)
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
mL82WA [auth Aq]341Leishmania majorMutation(s): 0 
Gene Names: LMJF_19_1230
Find proteins for Q4QD92 (Leishmania major)
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
mL98XA [auth BE]118Leishmania majorMutation(s): 0 
Gene Names: LMJF_18_0260
Find proteins for Q4QE16 (Leishmania major)
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
mL73YA [auth Ak]323Leishmania majorMutation(s): 0 
Gene Names: LMJF_17_0760
Find proteins for Q4QEC8 (Leishmania major)
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
mL52,mL52ZA [auth BP]254Leishmania majorMutation(s): 0 
Gene Names: LMJF_13_0140
Find proteins for Q4QGE0 (Leishmania major)
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
mL49AB [auth Ad]237Leishmania majorMutation(s): 0 
Gene Names: LMJF_08_0560
Find proteins for Q4QIB3 (Leishmania major)
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
mL99BB [auth BF]109Leishmania majorMutation(s): 0 
Gene Names: LMJF_07_0420
Find proteins for Q4QIQ1 (Leishmania major)
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
mL88CB [auth Av]192Leishmania majorMutation(s): 0 
Gene Names: LMJF_07_0070
Find proteins for Q4QIT7 (Leishmania major)
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
mL63DB [auth Af]155Leishmania majorMutation(s): 0 
Gene Names: LMJF_05_0860
Find proteins for Q4QJB6 (Leishmania major)
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
mL85EB [auth As]249Leishmania majorMutation(s): 0 
Gene Names: LMJF_01_0060
Find proteins for E9ABZ5 (Leishmania major)
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
mL53FB [auth Ae]311Leishmania majorMutation(s): 0 
Gene Names: LMJF_03_0150
Find proteins for E9ACG2 (Leishmania major)
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
MRP-L46 domain-containing proteinGB [auth Ac]291Leishmania majorMutation(s): 0 
Gene Names: LMJF_06_0040
Find proteins for Q4QJ75 (Leishmania major)
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
mL68HB [auth Ah]570Leishmania majorMutation(s): 0 
Gene Names: LMJF_21_1500
Find proteins for Q4QC45 (Leishmania major)
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
mL97IB [auth BD]102Leishmania majorMutation(s): 0 
Gene Names: LMJF_18_0310
Find proteins for Q4QE11 (Leishmania major)
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
C2H2-type domain-containing proteinJB [auth Ay]174Leishmania majorMutation(s): 0 
Gene Names: LMJF_29_0360
Find proteins for E9ADN7 (Leishmania major)
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
mL54/69KB [auth Ag]244Leishmania majorMutation(s): 0 
Gene Names: LMJF_28_2360
Find proteins for Q4Q829 (Leishmania major)
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
LIM zinc-binding domain-containing proteinLB [auth Ax]216Leishmania majorMutation(s): 0 
Gene Names: LMJF_30_0280
Find proteins for Q4Q7T1 (Leishmania major)
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
Putative ribosomal protein L2MB [auth BL]380Leishmania majorMutation(s): 0 
Gene Names: LMJF_08_0280
Find proteins for Q4QIE1 (Leishmania major)
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
Putative ribosomal protein L14NB [auth BO]190Leishmania majorMutation(s): 0 
Gene Names: LMJF_34_3815
Find proteins for Q4Q2G1 (Leishmania major)
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
mL100OB [auth BG]1347Leishmania majorMutation(s): 0 
Find proteins for A0A504WW14 (Leishmania donovani)
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
UBPB [auth UB]67Leishmania majorMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
UCQB [auth UC]144Leishmania majorMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
UDRB [auth UD]95Leishmania majorMutation(s): 0 
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Entity ID: 71
MoleculeChainsLengthOrganismImage
Ribosomal RNASB [auth 1]9070Leishmania major
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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