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- PDB-6az3: Cryo-EM structure of of the large subunit of Leishmania ribosome ... -

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Basic information

Entry
Database: PDB / ID: 6az3
TitleCryo-EM structure of of the large subunit of Leishmania ribosome bound to paromomycin
Components
  • (ribosomal protein ...) x 42
  • rRNA 5.8S
  • rRNA 5S
  • rRNA alpha
  • rRNA beta
  • rRNA delta
  • rRNA epsilon
  • rRNA gamma
  • rRNA zeta
KeywordsRIBOSOME/ANTIBIOTIC / Leishmania / ribosome / aminoglycoside / paromomycin / RIBOSOME-ANTIBIOTIC complex
Function / homologyRibosomal protein L21 superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L38e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L40e superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal protein L14p/L23e ...Ribosomal protein L21 superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L38e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L40e superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L10e/L16 superfamily / Ubiquitin family / Ribosomal protein L16p/L10e / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L30p/L7e / Ribosomal protein L6 / KOW motif / Ribosomal protein L36e domain superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / ribosomal L5P family C-terminus / Ribosomal protein L5, N-terminal / 60S ribosomal protein L4, C-terminal domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L28e/Mak16 / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L19, eukaryotic / Ribosomal protein L14 superfamily / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L32e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L4/L1 family / Ribosomal L15 / Ribosomal protein L21e signature. / Ribosomal protein L39e signature. / Ribosomal L30 N-terminal domain / Ribosomal L18 C-terminal region / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ubiquitin domain signature. / Ribosomal protein L37e / Ribosomal protein L5 signature. / Ribosomal protein L22 signature. / Ribosomal protein L30 signature. / Ribosomal protein L6 signature 2. / Ribosomal protein L30e signature 1. / Ribosomal protein L1e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L14 / Ribosomal L38e protein family / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L34e / Ribosomal L29 protein / Ribosomal L39 protein / Ribosomal protein L44 / Ribosomal L40e family / Ribosomal protein L21e / Ribosomal protein L36e / Ribosomal protein L31e / Ribosomal protein L35Ae / Ribosomal L37ae protein family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L19e / Ribosomal protein L32 / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L22e protein family / Ribosomal L27e protein family / Ribosomal L28e protein family / Ribosomal L29e protein family / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L4/L1e / Ribosomal protein L37e / Ribosomal protein L35A / Ribosomal protein L29/L35 / Ribosomal protein L7A/L8 / Ribosomal protein L40e / Ribosomal protein L5 / Ribosomal protein L6, conserved site-2 / Ribosomal protein L10e / Ribosomal protein L22e / Ribosomal protein L28e / Ribosomal protein L29e / Ribosomal protein L37ae / Ribosomal protein L38e / Ribosomal protein L14e domain / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L32e / Ribosomal protein L21e
Function and homology information
Specimen sourceLeishmania donovani (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 2.5 Å resolution
AuthorsShalev-Benami, M. / Zhang, Y. / Rozenberg, H. / Nobe, Y. / Taoka, M. / Matzov, D. / Zimmerman, E. / Bashan, A. / Isobe, T. / Jaffe, C.L. / Yonath, A. / Skiniotis, G.
CitationJournal: Nat Commun / Year: 2017
Title: Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin.
Authors: Moran Shalev-Benami / Yan Zhang / Haim Rozenberg / Yuko Nobe / Masato Taoka / Donna Matzov / Ella Zimmerman / Anat Bashan / Toshiaki Isobe / Charles L Jaffe / Ada Yonath / Georgios Skiniotis
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 9, 2017 / Release: Dec 6, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 6, 2017Structure modelrepositoryInitial release
1.1Dec 13, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Assembly

Deposited unit
A: ribosomal protein uL2
B: ribosomal protein uL3
C: ribosomal protein uL4
D: ribosomal protein uL5
E: ribosomal protein uL6
F: ribosomal protein eL6
G: ribosomal protein eL8
H: ribosomal protein uL13
I: ribosomal protein eL13
J: ribosomal protein uL14
K: ribosomal protein eL14
L: ribosomal protein uL15
M: ribosomal protein eL15
N: ribosomal protein uL16
O: ribosomal protein uL18
P: ribosomal protein eL18
Q: ribosomal protein eL19
R: ribosomal protein eL20
S: ribosomal protein eL21
T: ribosomal protein uL22
U: ribosomal protein eL22
V: ribosomal protein uL23
W: ribosomal protein uL24
X: ribosomal protein eL24
Y: ribosomal protein eL27
Z: ribosomal protein eL28
a: ribosomal protein uL29
b: ribosomal protein eL29
c: ribosomal protein uL30
d: ribosomal protein eL30
e: ribosomal protein eL31
f: ribosomal protein eL32
g: ribosomal protein eL33
h: ribosomal protein eL34
i: ribosomal protein eL36
j: ribosomal protein eL37
k: ribosomal protein eL38
l: ribosomal protein eL39
m: ribosomal protein eL40
n: ribosomal protein eL41
o: ribosomal protein eL43
p: ribosomal protein eL44
1: rRNA alpha
2: rRNA beta
3: rRNA gamma
4: rRNA delta
5: rRNA epsilon
6: rRNA zeta
7: rRNA 5.8S
8: rRNA 5S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,119,81395
Polyers2,112,50750
Non-polymers7,30645
Water18,3571019
1


  • idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)501950
ΔGint (kcal/M)-3861
Surface area (Å2)579000

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Components

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Ribosomal protein ... , 42 types, 42 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#1: Protein/peptide ribosomal protein uL2 /


Mass: 27520.994 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote)
#2: Protein/peptide ribosomal protein uL3 /


Mass: 45741.395 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote)
#3: Protein/peptide ribosomal protein uL4 /


Mass: 40523.211 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BKR3
#4: Protein/peptide ribosomal protein uL5 /


Mass: 19245.344 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BFL1
#5: Protein/peptide ribosomal protein uL6 /


Mass: 21118.717 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BFB5
#6: Protein/peptide ribosomal protein eL6 /


Mass: 21208.869 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote)
#7: Protein/peptide ribosomal protein eL8 /


Mass: 39175.203 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B949
#8: Protein/peptide ribosomal protein uL13 /


Mass: 25346.008 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote)
#9: Protein/peptide ribosomal protein eL13 /


Mass: 23897.861 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote)
#10: Protein/peptide ribosomal protein uL14 /


Mass: 14421.971 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BSQ4
#11: Protein/peptide ribosomal protein eL14 /


Mass: 17038.955 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: Q25278
#12: Protein/peptide ribosomal protein uL15 /


Mass: 16034.684 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BSQ2
#13: Protein/peptide ribosomal protein eL15 /


Mass: 24366.773 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BMB4
#14: Protein/peptide ribosomal protein uL16 /


Mass: 24607.186 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B840
#15: Protein/peptide ribosomal protein uL18 /


Mass: 34100.633 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BS61
#16: Protein/peptide ribosomal protein eL18 /


Mass: 21939.883 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BUI1
#17: Protein/peptide ribosomal protein eL19 /


Mass: 22901.018 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B8Q2
#18: Protein/peptide ribosomal protein eL20 /


Mass: 20703.172 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BRT7
#19: Protein/peptide ribosomal protein eL21 /


Mass: 17437.443 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BRE2
#20: Protein/peptide ribosomal protein uL22 /


Mass: 17828.902 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BGL6
#21: Protein/peptide ribosomal protein eL22 /


Mass: 14042.504 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BU52
#22: Protein/peptide ribosomal protein uL23 /


Mass: 13461.783 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B8R9
#23: Protein/peptide ribosomal protein uL24 /


Mass: 13874.408 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote)
#24: Protein/peptide ribosomal protein eL24 /


Mass: 7988.512 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote)
#25: Protein/peptide ribosomal protein eL27 /


Mass: 15223.005 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BP34
#26: Protein/peptide ribosomal protein eL28 /


Mass: 15525.923 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BAU9
#27: Protein/peptide ribosomal protein uL29 /


Mass: 14987.824 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BIP6
#28: Protein/peptide ribosomal protein eL29 /


Mass: 7788.074 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BU64
#29: Protein/peptide ribosomal protein uL30 /


Mass: 26313.074 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BI29
#30: Protein/peptide ribosomal protein eL30 /


Mass: 10122.675 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BRQ6
#31: Protein/peptide ribosomal protein eL31 /


Mass: 13503.024 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BSK4
#32: Protein/peptide ribosomal protein eL32 /


Mass: 15029.650 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BFJ5
#33: Protein/peptide ribosomal protein eL33 /


Mass: 14336.777 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BR22
#34: Protein/peptide ribosomal protein eL34 /


Mass: 14640.328 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BUA1
#35: Protein/peptide ribosomal protein eL36 /


Mass: 11050.092 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BF65
#36: Protein/peptide ribosomal protein eL37 /


Mass: 9531.135 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: P62885
#37: Protein/peptide ribosomal protein eL38 /


Mass: 8761.474 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B7P2
#38: Protein/peptide ribosomal protein eL39 /


Mass: 6373.649 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BCX6
#39: Protein/peptide ribosomal protein eL40 /


Mass: 5912.278 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BMW6
#40: Protein/peptide ribosomal protein eL41 /


Mass: 4259.300 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote)
#41: Protein/peptide ribosomal protein eL43 /


Mass: 10092.869 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BFK4
#42: Protein/peptide ribosomal protein eL44 /


Mass: 11141.353 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BBL5

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RNA chain , 8 types, 8 molecules 12345678

#43: RNA chain rRNA alpha


Mass: 575707.562 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 322500086
#44: RNA chain rRNA beta


Mass: 492460.781 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 322500086
#45: RNA chain rRNA gamma


Mass: 67568.750 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 322500086
#46: RNA chain rRNA delta


Mass: 59144.129 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 5019758
#47: RNA chain rRNA epsilon


Mass: 42869.438 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 5019758
#48: RNA chain rRNA zeta


Mass: 22725.590 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 5019758
#49: RNA chain rRNA 5.8S


Mass: 54989.570 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 1229082208
#50: RNA chain rRNA 5S


Mass: 37923.516 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 1229082190

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Non-polymers , 4 types, 1064 molecules

#51: Chemical
ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 10 / Formula: C23H45N5O14 / Paromomycin
#52: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 34 / Formula: Mg / Magnesium
#53: Chemical ChemComp-C / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Formula: C9H14N3O8P / Cytidine monophosphate
#54: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1019 / Formula: H2O / Water

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Leishmania donovani 91S ribosome LSU / Type: RIBOSOME
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50
Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
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

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 141028 / Symmetry type: POINT

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