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- EMDB-6788: Small subunit of Trichomonas vaginalis ribosome -

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Basic information

Entry
Database: EMDB / ID: 6788
TitleSmall subunit of Trichomonas vaginalis ribosome
Map data
SampleSmall subunit of Trichomonas vaginalis ribosome
  • nucleic-acidNucleic acid
  • (40S ribosomal protein ...) x 15
  • (Ribosomal protein ...) x 10
  • (Uncharacterized ...) x 5
  • Plectin/S10 domain containing protein
  • Guanine nucleotide-binding protein beta subunit, putative
  • eL41
Function / homologyRibosomal protein S2, eukaryotic / Ribosomal protein S8 superfamily / Ribosomal protein S7 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal ...Ribosomal protein S2, eukaryotic / Ribosomal protein S8 superfamily / Ribosomal protein S7 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / WD40-repeat-containing domain superfamily / Ribosomal protein S19, superfamily / Winged helix-like DNA-binding 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 / RNA-binding S4 domain superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S15P / Ribosomal protein S19e domain superfamily / Ribosomal protein S17e, conserved site / K homology domain-like, alpha/beta / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S4/S9 / WD40 repeat, conserved site / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / 40S Ribosomal protein S10 / Ribosomal protein S4e, central domain superfamily / Ribosomal protein L2, domain 2 / S25 ribosomal protein / 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 / Plectin/S10 domain / Ribosomal protein S6e / Ribosomal protein S5, C-terminal domain / Ribosomal protein S30 / Ribosomal protein L41 / KH domain / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S28e / Ribosomal protein S19e / Ribosomal protein S26e superfamily / Ribosomal protein S2 / Ribosomal protein S21e superfamily / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein S19 / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S5, N-terminal domain / Ribosomal S3Ae family / 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 / Ribosomal family S4e / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S8 signature. / Ribosomal protein S27e / Ribosomal protein S11 signature. / Ribosomal protein S5/S7 / Ribosomal protein S17/S11 / Ribosomal protein S28e / Ribosomal protein S12e / Ribosomal protein S7e / Ribosomal protein S15 / Ribosomal protein S8 / Ribosomal protein S17 signature.
Function and homology information
SourceTrichomonas vaginalis (eukaryote)
Methodsingle particle reconstruction / cryo EM / 3.35 Å resolution
AuthorsLi Z / Guo Q
CitationJournal: Cell Res. / Year: 2017
Title: Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii.
Authors: Zhifei Li / Qiang Guo / Lvqin Zheng / Yongsheng Ji / Yi-Ting Xie / De-Hua Lai / Zhao-Rong Lun / Xun Suo / Ning Gao
Validation ReportPDB-ID: 5xyi

SummaryFull reportAbout validation report
DateDeposition: Jul 8, 2017 / Header (metadata) release: Aug 30, 2017 / Map release: Aug 30, 2017 / Last update: Oct 18, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.036
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.036
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5xyi
  • Surface level: 0.036
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6788.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.32 Å/pix.
= 422.4 Å
320 pix
1.32 Å/pix.
= 422.4 Å
320 pix
1.32 Å/pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.036 (by author), 0.036 (movie #1):
Minimum - Maximum-0.13911201 - 0.26773617
Average (Standard dev.)0.00029812296 (0.005232952)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 422.40002 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z422.400422.400422.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1390.2680.000

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Supplemental data

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Mask #1

Fileemd_6788_msk_1.map ( map file in CCP4 format, 131073 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1

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Mask #1~

Fileemd_6788_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Small subunit of Trichomonas vaginalis ribosome

EntireName: Small subunit of Trichomonas vaginalis ribosome / Number of components: 35

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Component #1: protein, Small subunit of Trichomonas vaginalis ribosome

ProteinName: Small subunit of Trichomonas vaginalis ribosome / Recombinant expression: No
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #2: nucleic-acid, 18S

Nucleic-acidName: 18S / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
ACUUGGUUGA UCCUGCCAAG GAAGCACACU UAGGUCAUAG AUUAAGCCAU GCAAGUGUUA GUUCAGGUAA CGAAACUGCG AAUAGCUCAU UAAUACGCUC AGAAUCUAUU UGGCGGCGAC CAACAGGUCU UAAAUGGAUA GCAGCAGCAA CUCUGGUGCU AAUACAUGCG AUUGUUUCUC CAGAUGUGAA UUAUGGAGGA AAAGUUGACC UCAUCAGAGG CACGCCAUUC GACUGAGUGA CCUAUCAGCU UGUACUUAGG GUCUUUACCU AGGUAGGCUA UCACGGGUAA CGGGCGGUUA CCGUCGGACU GCCGGAGAAG GCGCCUGAGA GAUAGCGACU AUAUCCACGG GUAGCAGCAG GCGCGAAACU UUCCCACUCG AGACUUUCGG AGGAGGUAAU GACCAGUUCC AUUGGUGCCU UUUGGUACUG UGGAUAGGGG UACGGUUUUC CACCGUACCG AAACCUAGCA GAGGGCCAGU CUGGUGCCAG CAGCUGCGGU AAUUCCAGCU CUGCGAGUUU GCUCCCAUAU UGUUGCAGUU AAAACGCCCG UAGUCUGAAU UGGCCAGCAA UGGUCGUACG UAUUUUUACG UUCACUGUGA ACAAAUCAGG ACGCUUAGAG UAUGGCCACA UGAAUGACUC AGCGCAGUAU GAAGUCUUUG UUUUCUUCCG AAAACAAGCU CAAUGAGAGC CAUCGGGGGU AGAUCUAUCU CAUGACGAGU GGUGGAAUAC UUUGACUCAU GAGAGAGAAG CUGAGGCGAA GGCGUCUACC UAGAGGGUUU CUGUCGAUCA AGGGCGAGAG UAGGAGUAUC CAACAGGAUU AGAGACCCUG GUAGUUCCUA CCUUAAACGA UGCCGACAGG AGUUUGUCAU UUGUUAAUGG CAGAAUCUUU GGAGAAAUCA UAGUUCUUGG GCUCUGGGGG AAAUACGACC GCAAGGCUGA AACUUGAAGG AAUUGACGGA AGGGCACACC AGGGGUGGAG CCUGUGGCUU AAUUUGAAUC AACACGGGGA AACUACCCAG GACCAGAUGU UUUUUAUGAC UGACAGGCUU CGGGUCUUUC AGGAUAUUGU UUUUGGUGGU GCAUGGCCGU UGGUGGUGCG UGGGUUGACC UGUCUAGCGU UGAUUCAGCU AACGAGCGAG AUUAUCGCCA AUUAUUUACU UUGCCGAAGU CCUUCGGUUA AAGUUCUAAU UGGGACUCCC UGCGAUUUUA GCAGGUGGAA GAGGGUAGCA AUAACAGGUC CGUGAUGCCC UUUAGAUGCU CUGGGCUGCA CGCGUGCUAC AAUGUUAGGA UCAAUAGGAC UGCGAGCCUG AGAGGGUGCG CUACUCUUAU AAUCCCUAAC GUAGUUGGGA UUGACGUUUG UAAUCAGCGU CAUGAACCAG GAAUCCCUUG UAAAUGUGUG UCAACAACGC ACGUUGAAUA CGUCCCUGCC CUUUGUACAC ACCGCCCGUC GCUCCUACCG AUUGGAUGAC UCGGUGAAAU CACCGGAUGC UUACGAGCAG AAAGUGAUUA AAUCACGUUA UCUAGAGGAA GGAGAAGUCG UAACAAGGUA ACGGUAGGUG AACCUGCCGU UGGAUCA
MassTheoretical: 508.656188 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #3: protein, 40S ribosomal protein SA

ProteinName: 40S ribosomal protein SA / Recombinant expression: No
MassTheoretical: 28.584676 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #4: protein, Ribosomal protein S3Ae, putative

ProteinName: Ribosomal protein S3Ae, putativeRibosome / Recombinant expression: No
MassTheoretical: 28.085471 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #5: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 30.083736 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #6: protein, Ribosomal protein S3, putative

ProteinName: Ribosomal protein S3, putativeRibosome / Recombinant expression: No
MassTheoretical: 24.505658 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #7: protein, 40S ribosomal protein S4

ProteinName: 40S ribosomal protein S4 / Recombinant expression: No
MassTheoretical: 28.589561 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #8: protein, 40s ribosomal protein S5-B, putative

ProteinName: 40s ribosomal protein S5-B, putativeRibosome / Recombinant expression: No
MassTheoretical: 21.672889 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #9: protein, 40S ribosomal protein S6

ProteinName: 40S ribosomal protein S6 / Recombinant expression: No
MassTheoretical: 24.583883 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #10: protein, 40S ribosomal protein S7, putative

ProteinName: 40S ribosomal protein S7, putativeRibosome / Recombinant expression: No
MassTheoretical: 18.708568 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #11: protein, 40S ribosomal protein S8

ProteinName: 40S ribosomal protein S8 / Recombinant expression: No
MassTheoretical: 22.118488 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #12: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 21.811295 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #13: protein, Plectin/S10 domain containing protein

ProteinName: Plectin/S10 domain containing protein / Recombinant expression: No
MassTheoretical: 16.251438 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #14: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 18.015252 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #15: protein, Ribosomal protein L7Ae, putative

ProteinName: Ribosomal protein L7Ae, putativeRibosome / Recombinant expression: No
MassTheoretical: 13.714954 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #16: protein, 40S ribosomal protein S13, putative

ProteinName: 40S ribosomal protein S13, putativeRibosome / Recombinant expression: No
MassTheoretical: 17.071031 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #17: protein, Ribosomal protein S14

ProteinName: Ribosomal protein S14 / Recombinant expression: No
MassTheoretical: 16.689012 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #18: protein, Ribosomal protein S19, putative

ProteinName: Ribosomal protein S19, putativeRibosome / Recombinant expression: No
MassTheoretical: 16.28608 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #19: protein, 40S ribosomal protein S16, putative

ProteinName: 40S ribosomal protein S16, putativeRibosome / Recombinant expression: No
MassTheoretical: 15.626175 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #20: protein, 40S ribosomal protein S17-B, putative

ProteinName: 40S ribosomal protein S17-B, putativeRibosome / Recombinant expression: No
MassTheoretical: 14.964434 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #21: protein, Ribosomal protein S13p/S18e, putative

ProteinName: Ribosomal protein S13p/S18e, putativeRibosome / Recombinant expression: No
MassTheoretical: 17.564523 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #22: protein, Ribosomal protein S19e, putative

ProteinName: Ribosomal protein S19e, putativeRibosome / Recombinant expression: No
MassTheoretical: 16.584188 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #23: protein, Ribosomal protein S10p/S20e, putative

ProteinName: Ribosomal protein S10p/S20e, putativeRibosome / Recombinant expression: No
MassTheoretical: 13.933201 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #24: protein, 40S ribosomal protein S21

ProteinName: 40S ribosomal protein S21 / Recombinant expression: No
MassTheoretical: 9.85313 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #25: protein, Ribosomal protein S15a

ProteinName: Ribosomal protein S15aRibosome / Recombinant expression: No
MassTheoretical: 14.583213 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #26: protein, 40S ribosomal protein S23, putative

ProteinName: 40S ribosomal protein S23, putativeRibosome / Recombinant expression: No
MassTheoretical: 15.592457 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #27: protein, Ribosomal protein S24e, putative

ProteinName: Ribosomal protein S24e, putativeRibosome / Recombinant expression: No
MassTheoretical: 16.069884 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #28: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 12.645859 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #29: protein, 40S ribosomal protein S26

ProteinName: 40S ribosomal protein S26 / Recombinant expression: No
MassTheoretical: 13.889256 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #30: protein, 40S ribosomal protein S27

ProteinName: 40S ribosomal protein S27 / Recombinant expression: No
MassTheoretical: 9.467907 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #31: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 7.650717 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #32: protein, 40S ribosomal protein S29, putative

ProteinName: 40S ribosomal protein S29, putativeRibosome / Recombinant expression: No
MassTheoretical: 6.8431 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #33: protein, 40S ribosomal protein S30

ProteinName: 40S ribosomal protein S30 / Recombinant expression: No
MassTheoretical: 6.919079 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #34: protein, Guanine nucleotide-binding protein beta subunit, putative

ProteinName: Guanine nucleotide-binding protein beta subunit, putative
Recombinant expression: No
MassTheoretical: 37.151832 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Component #35: protein, eL41

ProteinName: eL41 / Recombinant expression: No
MassTheoretical: 3.354243 kDa
SourceSpecies: Trichomonas vaginalis (eukaryote)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
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: 2 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: 57162
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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