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- PDB-5t2a: CryoEM structure of the Leishmania donovani 80S ribosome at 2.9 A... -

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Basic information

Entry
Database: PDB / ID: 5t2a
TitleCryoEM structure of the Leishmania donovani 80S ribosome at 2.9 Angstrom resolution
Components
  • 18S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • LSU-alpha
  • LSU-beta
  • RACK1
  • eL13
  • eL14
  • eL15
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL24
  • eL27
  • eL28
  • eL29
  • eL30
  • eL31
  • eL32
  • eL33
  • eL34
  • eL36
  • eL37
  • eL38
  • eL39
  • eL40
  • eL42
  • eL43
  • eL6
  • eL8
  • eS1
  • eS10
  • eS17
  • eS19
  • eS21
  • eS24
  • eS26
  • eS27
  • eS28
  • eS30
  • eS4
  • eS6
  • eS7
  • eS8
  • srRNA1
  • srRNA2
  • srRNA3
  • srRNA4
  • uL13
  • uL14
  • uL15
  • uL16
  • uL18
  • uL2
  • uL22
  • uL23
  • uL24
  • uL29
  • uL3
  • uL30
  • uL4
  • uL5
  • uL6
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS17
  • uS19
  • uS2
  • uS3
  • uS4
  • uS5
  • uS7
  • uS8
  • uS9
KeywordsRIBOSOME / Leishmania donovani
Function / homology
Function and homology information


protein-RNA complex assembly / translation regulator activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit biogenesis / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding ...protein-RNA complex assembly / translation regulator activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit biogenesis / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / nucleolus / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L28e / Ribosomal protein L23 / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily ...Ribosomal protein L28e / Ribosomal protein L23 / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Ribosomal protein L10e, conserved site / Plectin/S10 domain / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L19, eukaryotic / Ribosomal protein S8e subdomain, eukaryotes / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L40e superfamily / 40S ribosomal protein S4 C-terminus / Ribosomal protein L30e signature 2. / Ribosomal protein S8e, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S8e signature. / Ribosomal protein L30e, conserved site / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L14e domain / 60S ribosomal protein L19 / Ribosomal protein L14 / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / Ribosomal protein L30/YlxQ / RS4NT (NUC023) domain / Ribosomal protein L7A/L8 / 60S ribosomal protein L35 / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein L14 / Ribosomal protein L14, KOW motif / Ribosomal protein L37ae / Ribosomal L37ae protein family / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L7, eukaryotic / Ribosomal_L19e / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein S8e / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein S3Ae / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal S3Ae family / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal S3Ae family
Similarity search - Domain/homology
: / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L23a ...: / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L23a / Ribosomal protein L38, putative / 60S ribosomal protein L10, putative / 60S ribosomal protein L19, putative / 60S ribosomal protein L7a / Large ribosomal subunit protein eL28 / 40S ribosomal protein S15A, putative / 40S ribosomal protein S4 / 60S ribosomal protein L44, putative / 60S ribosomal protein L39, putative / 60S ribosomal protein L9, putative / 60S ribosomal protein L37a / 60S ribosomal protein L11 (L5, L16) / 60S ribosomal protein L17, putative / 40S ribosomal protein S8 / 60S ribosomal protein L7, putative / 40S ribosomal protein S16, putative / 60S ribosomal protein L35, putative / Ribosomal protein S10 / Ribosomal protein S29, putative / Ribosomal protein L1a, putative / 40S ribosomal protein S30 / Ribosomal protein L15 / Ubiquitin-ribosomal protein eL40 fusion protein / Ribosomal L27e family protein / Ribosomal protein L35Ae family protein / 40S ribosomal protein S19 protein, putative / 60S ribosomal protein L21, putative / 60S ribosomal protein L30 / Small ribosomal subunit protein eS1 / 60S ribosomal protein L18a / 60S ribosomal protein L5, putative / 60S ribosomal protein L36, Putative / 60S ribosomal protein L32 / 60S ribosomal subunit protein L31, putative / 60S ribosomal protein L27A/L29, putative / 60S ribosomal protein L23, putative / 40S ribosomal protein S18, putative / 40S ribosomal protein S10, putative / 40S ribosomal protein S9, putative / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL34 / 60S ribosomal protein L18, putative / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL14 / 40S ribosomal protein S5 / LACK protective antigen
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhang, X. / Lai, M. / Zhou, Z.H.
CitationJournal: Nat Commun / Year: 2016
Title: Structures and stabilization of kinetoplastid-specific split rRNAs revealed by comparing leishmanial and human ribosomes.
Authors: Xing Zhang / Mason Lai / Winston Chang / Iris Yu / Ke Ding / Jan Mrazek / Hwee L Ng / Otto O Yang / Dmitri A Maslov / Z Hong Zhou /
Abstract: The recent success in ribosome structure determination by cryoEM has opened the door to defining structural differences between ribosomes of pathogenic organisms and humans and to understand ribosome- ...The recent success in ribosome structure determination by cryoEM has opened the door to defining structural differences between ribosomes of pathogenic organisms and humans and to understand ribosome-targeting antibiotics. Here, by direct electron-counting cryoEM, we have determined the structures of the Leishmania donovani and human ribosomes at 2.9 Å and 3.6 Å, respectively. Our structure of the leishmanial ribosome elucidates the organization of the six fragments of its large subunit rRNA (as opposed to a single 28S rRNA in most eukaryotes, including humans) and reveals atomic details of a unique 20 amino acid extension of the uL13 protein that pins down the ends of three of the rRNA fragments. The structure also fashions many large rRNA expansion segments. Direct comparison of our human and leishmanial ribosome structures at the decoding A-site sheds light on how the bacterial ribosome-targeting drug paromomycin selectively inhibits the eukaryotic L. donovani, but not human, ribosome.
History
DepositionAug 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.name

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: LSU-alpha
B: LSU-beta
C: 5.8S rRNA
D: 5S rRNA
E: srRNA1
F: srRNA3
G: srRNA2
H: srRNA4
I: eL18
J: uL16
K: uL5
L: eL13
M: uL13
N: eL14
O: eL15
P: uL22
Q: eL20
R: eL19
S: eL21
T: eL22
U: uL14
V: uL23
W: eL24
X: uL24
Y: eL27
Z: uL15
a: eL28
b: eL29
c: uL2
d: uL3
e: eL30
f: eL31
g: eL32
h: eL34
i: uL29
j: eL33
k: eL36
l: eL37
m: eL43
n: eL38
o: eL39
p: uL4
q: eL40
r: eL42
s: uL18
t: eL6
u: uL30
v: eL8
w: uL6
0: eS1
1: eS4
2: 18S rRNA
3: eS6
4: eS7
5: eS8
6: uS4
7: RACK1
8: uS14
AC: uS2
AD: eS10
AE: uS17
AG: uS15
AH: uS11
AI: uS19
AJ: uS8
AK: uS9
AL: eS17
AM: uS13
AN: uS7
AO: eS19
AP: uS5
AQ: uS10
AR: eS21
AS: uS12
AT: eS24
AV: eS26
AW: eS27
AX: uS3
AY: eS30
AZ: eS28


Theoretical massNumber of molelcules
Total (without water)3,469,65280
Polymers3,469,65280
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 9 types, 9 molecules ABCDEFGH2

#1: RNA chain LSU-alpha


Mass: 576313.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 322500086
#2: RNA chain LSU-beta


Mass: 471465.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#3: RNA chain 5.8S rRNA


Mass: 84351.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 79677111
#4: RNA chain 5S rRNA


Mass: 38532.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 361050153
#5: RNA chain srRNA1


Mass: 68191.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 322500086
#6: RNA chain srRNA3


Mass: 23360.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#7: RNA chain srRNA2


Mass: 59084.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 5019758
#8: RNA chain srRNA4


Mass: 40965.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 5019758
#52: RNA chain 18S rRNA


Mass: 710272.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 9504

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Protein , 71 types, 71 molecules IJKLMNOPQRSTUVWXYZabcdefghijkl...

#9: Protein eL18 / 60S ribosomal protein L18


Mass: 22071.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BUI1
#10: Protein uL16 / 60S ribosomal protein L10


Mass: 24607.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B840
#11: Protein uL5 / 60S ribosomal protein L11 (L5 / L16)


Mass: 21710.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BFL1
#12: Protein eL13


Mass: 24831.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#13: Protein uL13


Mass: 25479.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#14: Protein eL14 / 60S ribosomal protein L14 / 23 kDa cell surface protein / LDP 23


Mass: 19935.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: Q25278
#15: Protein eL15 / Ribosomal protein L15


Mass: 24497.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BMB4
#16: Protein uL22 / 60S ribosomal protein L17


Mass: 19154.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BGL6
#17: Protein eL20 / 60S ribosomal protein L18a


Mass: 20834.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BRT7
#18: Protein eL19 / 60S ribosomal protein L19


Mass: 28142.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B8Q2
#19: Protein eL21 / 60S ribosomal protein L21


Mass: 18059.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BRE2
#20: Protein eL22 / 60S ribosomal protein L22


Mass: 15030.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BU52
#21: Protein uL14 / 60S ribosomal protein L23


Mass: 14982.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BSQ4
#22: Protein uL23 / 60S ribosomal protein L23a


Mass: 16306.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: D1M863
#23: Protein eL24


Mass: 14608.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#24: Protein uL24


Mass: 16224.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#25: Protein eL27 / Ribosomal protein L27


Mass: 15455.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BP34
#26: Protein uL15 / 60S ribosomal protein L27A/L29


Mass: 16165.880 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BSQ2
#27: Protein eL28 / 60S ribosomal protein L28


Mass: 16409.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BAU9
#28: Protein eL29 / Ribosomal protein L29


Mass: 8001.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#29: Protein uL2


Mass: 28321.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#30: Protein uL3


Mass: 47593.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#31: Protein eL30 / 60S ribosomal protein L30


Mass: 11400.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BRQ6
#32: Protein eL31 / 60S ribosomal subunit protein L31


Mass: 20886.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BSK4
#33: Protein eL32 / 60S ribosomal protein L32


Mass: 15397.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BS76
#34: Protein eL34 / 60S ribosomal protein L34


Mass: 19307.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BUA1
#35: Protein uL29 / 60S ribosomal protein L35


Mass: 15232.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BIP6
#36: Protein eL33 / Ribosomal protein l35a


Mass: 16492.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BR22
#37: Protein eL36 / 60S Ribosomal protein L36


Mass: 11959.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BS63
#38: Protein eL37 / 60S ribosomal protein L37


Mass: 9862.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: P62885
#39: Protein eL43 / 60S ribosomal protein L37a


Mass: 10337.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BFK4
#40: Protein eL38 / Ribosomal protein L38


Mass: 9479.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B7P2
#41: Protein eL39 / 60S ribosomal protein L39


Mass: 6504.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BCX6
#42: Protein uL4 / Ribosomal protein L1a


Mass: 41228.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BKR3
#43: Protein eL40


Mass: 14711.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BMW6
#44: Protein eL42 / 60S ribosomal protein L44


Mass: 12302.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BBL5
#45: Protein uL18 / 60S ribosomal protein L5


Mass: 34100.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BS61
#46: Protein eL6


Mass: 21088.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#47: Protein uL30 / 60S ribosomal protein L7


Mass: 28915.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BI29
#48: Protein eL8 / 60S ribosomal protein L7a


Mass: 39175.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B949
#49: Protein uL6 / 60S ribosomal protein L9


Mass: 21567.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BFB5
#50: Protein eS1 / 40S ribosomal protein S3a


Mass: 30062.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BRS2
#51: Protein eS4 / 40S ribosomal protein S4


Mass: 30711.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BBI6
#53: Protein eS6


Mass: 28370.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#54: Protein eS7


Mass: 23765.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#55: Protein eS8 / 40S ribosomal protein S8


Mass: 25066.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BH78
#56: Protein uS4 / 40S ribosomal protein S9


Mass: 22184.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BTJ0
#57: Protein RACK1 / LACK protective antigen


Mass: 34459.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: Q9BIJ5
#58: Protein uS14 / Ribosomal protein S29


Mass: 6696.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BJV7
#59: Protein uS2


Mass: 27536.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#60: Protein eS10 / 40S ribosomal protein S10


Mass: 17432.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BTG4
#61: Protein uS17


Mass: 19981.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#62: Protein uS15 / 40S ribosomal protein S13


Mass: 17482.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#63: Protein uS11 / 40S ribosomal protein S14


Mass: 15623.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#64: Protein uS19


Mass: 17472.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#65: Protein uS8 / 40S ribosomal protein S15A


Mass: 14719.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BAV6
#66: Protein uS9 / 40S ribosomal protein S16


Mass: 16718.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BI96
#67: Protein eS17


Mass: 16447.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#68: Protein uS13 / 40S ribosomal protein S18


Mass: 17443.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BTF9
#69: Protein uS7


Mass: 21336.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: Q868B1
#70: Protein eS19 / 40S ribosomal protein S19 protein


Mass: 20188.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BR60
#71: Protein uS5


Mass: 28851.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#72: Protein uS10 / Ribosomal protein S20


Mass: 13031.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BJI2
#73: Protein eS21


Mass: 17102.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#74: Protein uS12


Mass: 15952.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#75: Protein eS24


Mass: 15910.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#76: Protein eS26 / Ribosomal protein S26


Mass: 12752.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#77: Protein eS27 / 40S ribosomal protein S27-1


Mass: 9803.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#78: Protein uS3


Mass: 24541.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#79: Protein eS30 / 40S ribosomal protein S30


Mass: 7394.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BLG3
#80: Protein eS28 / 40S ribosomal protein S33


Mass: 9705.151 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Leishmania donovani 80S ribosome / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Leishmania donovani (eukaryote)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 20 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
4CTFFINDCTF correction
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213108 / Symmetry type: POINT

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