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- EMDB-7024: Cryo-EM structure of the small subunit of Leishmania ribosome bou... -

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Basic information

Entry
Database: EMDB / ID: 7024
TitleCryo-EM structure of the small subunit of Leishmania ribosome bound to paromomycin
Map dataprimary map
SampleLeishmania donovani 91S ribosome SSU:
(ribosomal protein ...) x 32 / LACK1 / (nucleic-acidNucleic acid) x 5 / (ligand) x 3
Function / homologyRibosomal protein S10 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 S10 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 S11 superfamily / RNA-binding S4 domain 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
SourceLeishmania donovani (eukaryote) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / 2.7 Å resolution
AuthorsShalev-Benami M / Zhang Y
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 ReportPDB-ID: 6az1

SummaryFull reportAbout validation report
DateDeposition: Sep 9, 2017 / Header (metadata) release: Dec 6, 2017 / Map release: Dec 6, 2017 / Last update: Dec 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6az1
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6az1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7024.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.02 Å/pix.
= 391.68 Å
384 pix
1.02 Å/pix.
= 391.68 Å
384 pix
1.02 Å/pix.
= 391.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.232303 - 0.3947016
Average (Standard dev.)0.00026962307 (0.015102799)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin000
Limit383383383
Spacing384384384
CellA=B=C: 391.68 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z391.680391.680391.680
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.2320.3950.000

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Supplemental data

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Sample components

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Entire Leishmania donovani 91S ribosome SSU

EntireName: Leishmania donovani 91S ribosome SSU / Number of components: 42

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Component #1: protein, Leishmania donovani 91S ribosome SSU

ProteinName: Leishmania donovani 91S ribosome SSU / Recombinant expression: No
SourceSpecies: Leishmania donovani (eukaryote)

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Component #2: protein, Ribosomal protein s1e

ProteinName: Ribosomal protein s1eRibosome / Recombinant expression: No
MassTheoretical: 30.092064 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #3: protein, ribosomal protein S2

ProteinName: ribosomal protein S2 / Recombinant expression: No
MassTheoretical: 27.564682 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #4: protein, ribosomal protein S3

ProteinName: ribosomal protein S3 / Recombinant expression: No
MassTheoretical: 24.511762 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #5: protein, ribosomal protein S4

ProteinName: ribosomal protein S4 / Recombinant expression: No
MassTheoretical: 22.184914 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #6: protein, ribosomal protein S4e

ProteinName: ribosomal protein S4eRibosome / Recombinant expression: No
MassTheoretical: 30.711088 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #7: protein, ribosomal protein S5

ProteinName: ribosomal protein S5 / Recombinant expression: No
MassTheoretical: 28.803186 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #8: protein, ribosomal protein S6e

ProteinName: ribosomal protein S6eRibosome / Recombinant expression: No
MassTheoretical: 28.341164 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #9: protein, ribosomal protein S7

ProteinName: ribosomal protein S7 / Recombinant expression: No
MassTheoretical: 21.311596 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #10: protein, ribosomal protein S7e

ProteinName: ribosomal protein S7eRibosome / Recombinant expression: No
MassTheoretical: 23.867316 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #11: protein, ribosomal protein S8

ProteinName: ribosomal protein S8 / Recombinant expression: No
MassTheoretical: 14.719258 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #12: protein, ribosomal protein S8e

ProteinName: ribosomal protein S8eRibosome / Recombinant expression: No
MassTheoretical: 25.038346 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #13: protein, ribosomal protein S9

ProteinName: ribosomal protein S9 / Recombinant expression: No
MassTheoretical: 16.718586 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #14: protein, ribosomal protein S10

ProteinName: ribosomal protein S10 / Recombinant expression: No
MassTheoretical: 13.049076 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #15: protein, ribosomal protein S10e

ProteinName: ribosomal protein S10eRibosome / Recombinant expression: No
MassTheoretical: 17.43291 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #16: protein, ribosomal protein S11

ProteinName: ribosomal protein S11 / Recombinant expression: No
MassTheoretical: 15.609088 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #17: protein, ribosomal protein S12

ProteinName: ribosomal protein S12 / Recombinant expression: No
MassTheoretical: 15.952654 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #18: protein, ribosomal protein S12e

ProteinName: ribosomal protein S12eRibosome / Recombinant expression: No
MassTheoretical: 15.611837 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #19: protein, ribosomal protein S13

ProteinName: ribosomal protein S13 / Recombinant expression: No
MassTheoretical: 17.443436 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #20: protein, ribosomal protein S14

ProteinName: ribosomal protein S14 / Recombinant expression: No
MassTheoretical: 6.696929 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #21: protein, ribosomal protein S15

ProteinName: ribosomal protein S15 / Recombinant expression: No
MassTheoretical: 17.45574 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #22: protein, ribosomal protein S17

ProteinName: ribosomal protein S17 / Recombinant expression: No
MassTheoretical: 19.985369 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #23: protein, ribosomal protein S17e

ProteinName: ribosomal protein S17eRibosome / Recombinant expression: No
MassTheoretical: 16.521465 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #24: protein, ribosomal protein S19

ProteinName: ribosomal protein S1940S ribosomal protein S19 / Recombinant expression: No
MassTheoretical: 17.528463 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #25: protein, ribosomal protein S19e

ProteinName: ribosomal protein S19eRibosome / Recombinant expression: No
MassTheoretical: 20.188588 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #26: protein, ribosomal protein S21e

ProteinName: ribosomal protein S21eRibosome / Recombinant expression: No
MassTheoretical: 16.669115 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #27: protein, ribosomal protein S24e

ProteinName: ribosomal protein S24eRibosome / Recombinant expression: No
MassTheoretical: 15.808882 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #28: protein, ribosomal protein S25e

ProteinName: ribosomal protein S25eRibosome / Recombinant expression: No
MassTheoretical: 13.071399 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #29: protein, ribosomal protein S26e

ProteinName: ribosomal protein S26eRibosome / Recombinant expression: No
MassTheoretical: 12.794251 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #30: protein, ribosomal protein S27e

ProteinName: ribosomal protein S27eRibosome / Recombinant expression: No
MassTheoretical: 9.819463 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #31: protein, ribosomal protein S28e

ProteinName: ribosomal protein S28eRibosome / Recombinant expression: No
MassTheoretical: 9.763191 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #32: protein, ribosomal protein S30e

ProteinName: ribosomal protein S30eRibosome / Recombinant expression: No
MassTheoretical: 7.394894 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #33: protein, ribosomal protein S31e

ProteinName: ribosomal protein S31eRibosome / Recombinant expression: No
MassTheoretical: 17.015727 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #34: protein, LACK1

ProteinName: LACK1 / Recombinant expression: No
MassTheoretical: 34.459523 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #35: nucleic-acid, ribosomal RNA 18S

Nucleic-acidName: ribosomal RNA 18S / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GAUCUGG(OMU)UG AUUCUGC(OMC)AG UAGUCAU(A2M)UG CU(OMU)GUUU(OMC)AA GGACUUAGCC AUGCAUGCCU CAGAAUCACU GCAUUUGCAG GAAUCUGCGC AUGGCUC(A2M)UU ACAUCAGACG UAAU(OMC)UGCCG CAAAAAUCUU GCGGUUUCCG CAAAAUUGGA UAACUUGGCG AAACGCCAAG CUAAUACAUG AACCAACCGG GUGUUCUCCA CUCCAGACGG UGGGCAACCA UCGUCGUGAG ACGCCCAGCG AAUGAAUGAC AGUAAAACCA AUGCCUUCAC UGGCAGUAAC ACCCAGCAGU GUUGACUCAA UUCAUUCCGU GCGAAAGCCG GCUUGUUCCG GCGUCUUUUG ACGAACAACU GCCCUAUCAG CUGGUGAUGG CCGUGUAGUG GACUGCCAUG GCGUUGACGG GAGCGGGGGA UUAGGGUUCG AUUCCGGAGA GGGAGCCUGA GAAAUAGCUA CCACUUCUAC GGAGGGCAGC AGGCGCGC(A2M)A AUUGCCCAAU GUCAAAACAA AACGAUGA(OMG)G CAGCGAAAAG AAAUAGAGUU GUCAGUCCAU UUGGAUUGUC AUUUCAAUGG GGGAUAUUUA AACCCAUCCA AUAUCGAGUA ACAAUUGGAG GACAAGUCUG GUGCCAGCAC CCGCGGUAAU UCCAGCUCCA AAAGCGUAUA UUAAUGCUGU (OMU)GCUGUU(A2M)AA GGGUUCGUAG UUGAACUGUG GGCUGUGCAG GUUUGUUCCU GGUCGUCCCG UCCAUGUCGG AUUUGGUGAC CCAGGCCCUU GCAGCCCGUG AACAUUCAAA GAAACAAGAA ACACGGGAGU GGUUCCUUUC CUGAUUUACG CAUGUCAUGC AUGCCAGGGG GCGUCCGUGA UUUUUUACUG UGACUAAAGA AGCGUGACUA AAGCAGUCAU UUGACUUGAA UUAGAAAGCA UGGGAUAACA A(A2M)GGAGCAGC CUCUAGGCUA CCGUUUCGGC UUUUGUUGGU UUUAAAGGUC UAUUGGAGAU UAUGGAGCUG UGCGACAAGU GCUUUCCCAU CGCAACCUCG GUUCGGUGUG UGGCGCCUUU GAGGGGUUUA GUGCGUCCGG UACGAGCUCC GGUUCGUCCG GCCGUAACGC CUUUUCAACU CACGGCCUCU AGGAAUGAAG GAGGGUAGUU CGGGGGAGAA CGUACUGGGG CGUCAGAGGU GAAAUUCUUA GACCGCACCA AGACGAACUA CAGCGAAGGC AUUCUUCAAG GAUACCUUCC UCAAUCAAGA ACCAAAGUGU GGAGAUCGAA GAUGAUUAGA GACCAUUGUA GUCCACACUG CAAACGAUGA CACCCAUGAA UUGGGGAUCU UAUGGGCCGG CCUGCGGCAG GGUUUACCCU GUGUCAGCAC CGCGCCCGCU UUUACCACCU UACGUAUCUU UUCUAUUCGG CCUUUACCGG CCACCCACGG GAAUAUCCUC AGCACGUUUU CUGUUUUUUC ACGCGAAAGC UUUGAGGUUA CAGUCUCAGG GGG(OMG)AGUACG UUCGCAA(OMG)AG UGAAACUUAA AGAAAUUGAC GGAAUGGCAC CACAAGACGU GGAGCGUGCG GUUUAAUU(M1Y)G AC(C4J)(5MC)AACAC(OMG) GGGAACUUUA CCAGAUCCGG ACAGGAUGAG GAUUGACAGA UUGAGUGUUC UUUCUCGAUU CCCUGAAUGG (OMU)G(OMG)UGCAUGG CCGCUUUUGG UCGGUG(OMG)AGU GAUUUGUUUG GUUGAUUCCG UCAACGGACG AGAUCCAAGC UGCCCAGUAG AAUUCAGAAU UGCCCAUAGG AUAGCAAACU CAUCGGCGGG UUUUACCCAA CGGUGGGCCG CAUUCGGUCG AAUUCU(OMU)CUC UGCGGGAUUC CUUUGUAAUU GCACAAGGUG AAAUUUUGGG CAACAGCA(OMG)G UC(OMU)GUGAUGC UCCUCAAUGU UCUGGGCGAC ACGC(OMG)(OMC)ACUA CAAUGUCAGU GAGAACAAGA AAAACGACUU UUGUCGAACC UACUUGAUCA AAAGAGUGGG GAAACCCCGG AAUCACAUAG ACUCACUUGG GACCGAGGAU UGCAAUUA(OMU)U GGUCGCGCAA CGAG(7MG)AAUGU CUCGUAGGCG CAGCUCAUCA (A2M)ACUGUGCCG AUUACGUCCC UGCCAUU(OMU)GU ACACACCG(4OC)C (5MC)GUCGUUGUU UCCGAUGAUG GUGCAAUACA GGUGAUCGGA CAGGCGGUGU UUUAUCCGCC CGAAAGUUCA CCGAUAUUU(OMC) UUCAAUAGAG (OMG)AAGCAAAAG UCGUAACAAG GUAGCUGUAG GUG(MA6)(MA6)CCUGC AGCUGGAUCA UUU
MassTheoretical: 710.287438 kDa
SourceSpecies: Leishmania donovani (eukaryote)

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Component #36: nucleic-acid, tRNA-Phe

Nucleic-acidName: tRNA-Phe / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCGCGGAUAG CUCAGUCGGU AGAGCAGGGG AUUGAA(MIA)AUC CCCGUGUCCU UGGUUCGAUU CCGAGUCCGC GCACCA
MassTheoretical: 24.601766 kDa

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Component #37: nucleic-acid, P-site tRNA

Nucleic-acidName: P-site tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCGGGGUGG AGCAGCCUGG UAGCUCGUCG GGCUCAUAAC CCGAAGAUCG UCGGUUCAAA UCCGGCCCCC GCAACCA
MassTheoretical: 24.786785 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #38: nucleic-acid, E-site tRNA

Nucleic-acidName: E-site tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCGCGGAUAG CUCAGUCGGU AGAGCAGGGG AUUGAAAAUC CCCGUGUCCU UGGUUCGAUU CCGAGUCCGC GCACCA
MassTheoretical: 24.485539 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #39: nucleic-acid, mRNA

Nucleic-acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CACCAUGUUC AAA
MassTheoretical: 4.085501 kDa

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Component #40: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #41: ligand, PAROMOMYCIN

LigandName: PAROMOMYCIN / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.615628 kDa

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Component #42: ligand, water

LigandName: water / Number of Copies: 262 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 141028
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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