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

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Basic information

Entry
Database: PDB / ID: 6az1
TitleCryo-EM structure of the small subunit of Leishmania ribosome bound to paromomycin
Components
  • (ribosomal protein ...) x 32
  • E-site tRNA
  • LACK1
  • P-site tRNA
  • mRNAMessenger RNA
  • ribosomal RNA 18S
  • tRNA-Phe
KeywordsRIBOSOME/ANTIBIOTIC / Leishmania donovani / ribosome / aminoglycoside / paromomycin / RIBOSOME-ANTIBIOTIC complex
Function / homologyRNA-binding S4 domain superfamily / Ribosomal protein S2 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein S19 / Ubiquitin family / Ribosomal protein S14p/S29e / Ribosomal protein S15 ...RNA-binding S4 domain superfamily / Ribosomal protein S2 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein S19 / Ubiquitin family / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S5, N-terminal domain / Ribosomal protein S21e superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S17 / Ribosomal protein S9/S16 / WD domain, G-beta repeat / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein S13/S18 / Ribosomal S17 / S27a-like superfamily / Ribosomal protein S26e superfamily / Ribosomal S3Ae family / WD40-repeat-containing domain superfamily / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein S4e, central domain superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S11 superfamily / 40S Ribosomal protein S10 / Ribosomal protein S19e domain superfamily / Ribosomal family S4e / Ribosomal protein S19e / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13 signature. / Ribosomal protein S17 signature. / Ribosomal protein S19 signature. / Ribosomal protein S9 signature. / Ribosomal protein S15 signature. / Ribosomal protein S24e signature. / Ribosomal protein S6e signature. / Ribosomal protein S5 signature. / Ribosomal protein S4 signature. / Trp-Asp (WD) repeats signature. / Ribosomal protein S11 signature. / Ribosomal protein S28e signature. / Ribosomal protein S2 signature 2. / Ribosomal protein S8e signature. / Ubiquitin domain profile. / Trp-Asp (WD) repeats profile. / Ribosomal protein S13 family profile. / Trp-Asp (WD) repeats circular profile. / Type-2 KH domain profile. / Ribosomal protein S12 signature. / Ribosomal protein S8 signature. / Ribosomal protein S6e / Ribosomal protein S27a / Ribosomal protein S28e / Ribosomal protein S8e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S21e / Ribosomal protein S7e / Ribosomal protein S24e / Ribosomal protein S26e / S4 domain / Ribosomal protein S27 / Ribosomal_S17 N-terminal / S25 ribosomal protein / Plectin/S10 domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S30 / KH domain / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S10 domain / Ribosomal protein S7 domain / S4 RNA-binding domain profile. / Ribosomal protein S19/S15 / Ribosomal protein S10 / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e / Ribosomal protein S11 / Ribosomal protein S24e / Ribosomal protein S27a / Ribosomal protein S3Ae / RNA-binding S4 domain
Function and homology information
Specimen sourceLeishmania donovani (eukaryote)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 2.7 Å resolution
AuthorsShalev-Benami, M. / Zhang, Y. / Rozenberg, H. / Matzov, D. / Zimmerman, E. / Bashan, A. / 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 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 ABCDEFGHIJKLMNOPQRSTUVWXYZabcdef

#1: Protein/peptide Ribosomal protein s1e / Ribosome


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


Mass: 27564.682 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A4IDS4*PLUS
#3: Protein/peptide ribosomal protein S3 /


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


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


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


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


Mass: 28341.164 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: O44012*PLUS
#8: Protein/peptide ribosomal protein S7 /


Mass: 21311.596 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A4HV05*PLUS
#9: Protein/peptide ribosomal protein S7e / Ribosome


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


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


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


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


Mass: 13049.076 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BJI2*PLUS
#14: Protein/peptide ribosomal protein S10e / Ribosome


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


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


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


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


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


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


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


Mass: 19985.369 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: Q9TXA6*PLUS
#22: Protein/peptide ribosomal protein S17e / Ribosome


Mass: 16521.465 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BJZ5
#23: Protein/peptide ribosomal protein S19 / 40S ribosomal protein S19


Mass: 17528.463 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BFQ0*PLUS
#24: Protein/peptide ribosomal protein S19e / Ribosome


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


Mass: 16669.115 Da / Num. of mol.: 1 / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BAR6*PLUS
#26: Protein/peptide ribosomal protein S24e / Ribosome


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


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


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


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


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


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


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

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Protein/peptide , 1 types, 1 molecules g

#33: Protein/peptide LACK1


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

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RNA chain , 5 types, 5 molecules 12345

#34: RNA chain ribosomal RNA 18S


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


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


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


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


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

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


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


Mass: 18.015 Da / Num. of mol.: 262 / 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 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 (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 / 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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