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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
SampleLeishmania donovani 91S ribosome SSU
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 /
Map dataprimary map
Methodsingle particle reconstruction, at 2.7 Å resolution
AuthorsShalev-Benami M / Zhang Y
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 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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3D viewer


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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 package.

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 / ドノバンリーシュマニア

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Component #2: protein, Ribosomal protein s1e

ProteinName: Ribosomal protein s1e / Recombinant expression: No
MassTheoretical: 30.092064 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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Component #6: protein, ribosomal protein S4e

ProteinName: ribosomal protein S4e / Recombinant expression: No
MassTheoretical: 30.711088 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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Component #8: protein, ribosomal protein S6e

ProteinName: ribosomal protein S6e / Recombinant expression: No
MassTheoretical: 28.341164 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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Component #10: protein, ribosomal protein S7e

ProteinName: ribosomal protein S7e / Recombinant expression: No
MassTheoretical: 23.867316 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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Component #12: protein, ribosomal protein S8e

ProteinName: ribosomal protein S8e / Recombinant expression: No
MassTheoretical: 25.038346 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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Component #15: protein, ribosomal protein S10e

ProteinName: ribosomal protein S10e / Recombinant expression: No
MassTheoretical: 17.43291 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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Component #18: protein, ribosomal protein S12e

ProteinName: ribosomal protein S12e / Recombinant expression: No
MassTheoretical: 15.611837 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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Component #23: protein, ribosomal protein S17e

ProteinName: ribosomal protein S17e / Recombinant expression: No
MassTheoretical: 16.521465 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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Component #24: protein, ribosomal protein S19

ProteinName: ribosomal protein S19 / Recombinant expression: No
MassTheoretical: 17.528463 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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Component #25: protein, ribosomal protein S19e

ProteinName: ribosomal protein S19e / Recombinant expression: No
MassTheoretical: 20.188588 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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Component #26: protein, ribosomal protein S21e

ProteinName: ribosomal protein S21e / Recombinant expression: No
MassTheoretical: 16.669115 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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Component #27: protein, ribosomal protein S24e

ProteinName: ribosomal protein S24e / Recombinant expression: No
MassTheoretical: 15.808882 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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Component #28: protein, ribosomal protein S25e

ProteinName: ribosomal protein S25e / Recombinant expression: No
MassTheoretical: 13.071399 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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Component #29: protein, ribosomal protein S26e

ProteinName: ribosomal protein S26e / Recombinant expression: No
MassTheoretical: 12.794251 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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Component #30: protein, ribosomal protein S27e

ProteinName: ribosomal protein S27e / Recombinant expression: No
MassTheoretical: 9.819463 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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Component #31: protein, ribosomal protein S28e

ProteinName: ribosomal protein S28e / Recombinant expression: No
MassTheoretical: 9.763191 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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Component #32: protein, ribosomal protein S30e

ProteinName: ribosomal protein S30e / Recombinant expression: No
MassTheoretical: 7.394894 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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Component #33: protein, ribosomal protein S31e

ProteinName: ribosomal protein S31e / Recombinant expression: No
MassTheoretical: 17.015727 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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Component #34: protein, LACK1

ProteinName: LACK1 / Recombinant expression: No
MassTheoretical: 34.459523 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

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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 / ドノバンリーシュマニア

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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 / bacteria / エシェリキア・コリ, 大腸菌 /

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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 / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #39: nucleic-acid, mRNA

Nucleic-acidName: mRNA / 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

Specimen stateparticle
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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