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- PDB-6az1: Cryo-EM structure of the small subunit of Leishmania ribosome bou... -

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Entry
Database: PDB / ID: 6az1
TitleCryo-EM structure of the small subunit of Leishmania ribosome bound to paromomycin
DescriptorLACK1/RNA Complex
(ribosomal protein ...) x 32
KeywordsRIBOSOME/ANTIBIOTIC / Leishmania donovani / ribosome / aminoglycoside / paromomycin / RIBOSOME-ANTIBIOTIC complex
Specimen sourceLeishmania donovani / eukaryote / ドノバンリーシュマニア
Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (2.7 Å resolution / Particle / Single particle)
AuthorsShalev-Benami, M. / Zhang, Y. / Rozenberg, H. / Matzov, D. / Zimmerman, E. / Bashan, A. / Jaffe, C.L. / Yonath, A. / Skiniotis, G.
CitationNat Commun, 2017, 8, 1589-1589

Nat Commun, 2017, 8, 1589-1589 Yorodumi Papers
Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin.
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 s1e
B: ribosomal protein S2
C: ribosomal protein S3
D: ribosomal protein S4
E: ribosomal protein S4e
F: ribosomal protein S5
G: ribosomal protein S6e
H: ribosomal protein S7
I: ribosomal protein S7e
J: ribosomal protein S8
K: ribosomal protein S8e
L: ribosomal protein S9
M: ribosomal protein S10
N: ribosomal protein S10e
O: ribosomal protein S11
P: ribosomal protein S12
Q: ribosomal protein S12e
R: ribosomal protein S13
S: ribosomal protein S14
T: ribosomal protein S15
U: ribosomal protein S17
V: ribosomal protein S17e
W: ribosomal protein S19
X: ribosomal protein S19e
Y: ribosomal protein S21e
Z: ribosomal protein S24e
a: ribosomal protein S25e
b: ribosomal protein S26e
c: ribosomal protein S27e
d: ribosomal protein S28e
e: ribosomal protein S30e
f: ribosomal protein S31e
g: LACK1
1: ribosomal RNA 18S
2: tRNA-Phe
3: P-site tRNA
4: E-site tRNA
5: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,416,66068
Polyers1,412,38338
Non-polymers4,27730
Water4,720262
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)233520
ΔGint (kcal/M)-1705
Surface area (Å2)417100

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Components

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Ribosomal protein ... , 32 types, 32 molecules ABCDEFGHIJ...

#1: Polypeptide(L)Ribosomal protein s1e


Mass: 30092.064 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BRS2
#2: Polypeptide(L)ribosomal protein S2


Mass: 27564.682 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani
#3: Polypeptide(L)ribosomal protein S3


Mass: 24511.762 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BQ25
#4: Polypeptide(L)ribosomal protein S4


Mass: 22184.914 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BTJ0
#5: Polypeptide(L)ribosomal protein S4e


Mass: 30711.088 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BBI6
#6: Polypeptide(L)ribosomal protein S5


Mass: 28803.186 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BNF0
#7: Polypeptide(L)ribosomal protein S6e


Mass: 28341.164 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani
#8: Polypeptide(L)ribosomal protein S7


Mass: 21311.596 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani
#9: Polypeptide(L)ribosomal protein S7e


Mass: 23867.316 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9B7A8
#10: Polypeptide(L)ribosomal protein S8


Mass: 14719.258 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BAV6
#11: Polypeptide(L)ribosomal protein S8e


Mass: 25038.346 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BH78
#12: Polypeptide(L)ribosomal protein S9


Mass: 16718.586 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BI96
#13: Polypeptide(L)ribosomal protein S10


Mass: 13049.076 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani
#14: Polypeptide(L)ribosomal protein S10e


Mass: 17432.910 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BTG4
#15: Polypeptide(L)ribosomal protein S11


Mass: 15609.088 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BMA8
#16: Polypeptide(L)ribosomal protein S12


Mass: 15952.654 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BFB6
#17: Polypeptide(L)ribosomal protein S12e


Mass: 15611.837 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BBC0
#18: Polypeptide(L)ribosomal protein S13


Mass: 17443.436 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BTF9
#19: Polypeptide(L)ribosomal protein S14


Mass: 6696.929 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BJV7
#20: Polypeptide(L)ribosomal protein S15


Mass: 17455.740 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BPR7
#21: Polypeptide(L)ribosomal protein S17


Mass: 19985.369 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani
#22: Polypeptide(L)ribosomal protein S17e


Mass: 16521.465 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BJZ5
#23: Polypeptide(L)ribosomal protein S19


Mass: 17528.463 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani
#24: Polypeptide(L)ribosomal protein S19e


Mass: 20188.588 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BR60
#25: Polypeptide(L)ribosomal protein S21e


Mass: 16669.115 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani
#26: Polypeptide(L)ribosomal protein S24e


Mass: 15808.882 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BU11
#27: Polypeptide(L)ribosomal protein S25e


Mass: 13071.399 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BHM6
#28: Polypeptide(L)ribosomal protein S26e


Mass: 12794.251 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BK95
#29: Polypeptide(L)ribosomal protein S27e


Mass: 9819.463 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BUA2
#30: Polypeptide(L)ribosomal protein S28e


Mass: 9763.191 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BIH3
#31: Polypeptide(L)ribosomal protein S30e


Mass: 7394.894 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BLG3
#32: Polypeptide(L)ribosomal protein S31e


Mass: 17015.727 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: E9BTC5

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Polypeptide(L) , 1 types, 1 molecules g

#33: Polypeptide(L)LACK1


Mass: 34459.523 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: UniProt: Q9BIJ5

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RNA chain , 5 types, 5 molecules 12345

#34: RNA chainribosomal RNA 18S


Mass: 710287.438 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani / References: GenBank: 322500086
#35: RNA chaintRNA-Phe


Mass: 24601.766 Da / Num. of mol.: 1 / Source: (synth.) Escherichia coli / References: GenBank: 1229082179
#36: RNA chainP-site tRNA


Mass: 24786.785 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 817573384
#37: RNA chainE-site tRNA


Mass: 24485.539 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 1229082179
#38: RNA chainmRNA


Mass: 4085.501 Da / Num. of mol.: 1 / Source: (synth.) Leishmania donovani

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Non-polymers , 3 types, 292 molecules

#39: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Formula: Mg
#40: Chemical
ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 6 / Formula: C23H45N5O14
#41: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Leishmania donovani 91S ribosome SSU / 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
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Leishmania donovani
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 FIELD
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev-2686_1692: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 141028 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01086381
ELECTRON MICROSCOPYf_angle_d1.166126481
ELECTRON MICROSCOPYf_dihedral_angle_d18.20947125
ELECTRON MICROSCOPYf_chiral_restr0.06115904
ELECTRON MICROSCOPYf_plane_restr0.0088580

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