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- EMDB-8621: The cryo-EM structure of YjeQ bound to the 30S subunit suggests a... -

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Entry
Database: EMDB / ID: EMD-8621
TitleThe cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly
Map data
SampleStructure of the 30S subunit in complex with YjeQ GTPase
  • nucleic-acidNucleic acid
  • (30S ribosomal protein ...) x 19
  • Small ribosomal subunit biogenesis GTPase RsgA
  • (ligand) x 2
Function / homology
Function and homology information


guanosine tetraphosphate binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / ribosomal small subunit biogenesis / transcription antitermination / negative regulation of translational initiation / four-way junction DNA binding / DNA-templated transcription, termination ...guanosine tetraphosphate binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / ribosomal small subunit biogenesis / transcription antitermination / negative regulation of translational initiation / four-way junction DNA binding / DNA-templated transcription, termination / translation repressor activity, mRNA regulatory element binding / positive regulation of translational fidelity / endodeoxyribonuclease activity / maintenance of translational fidelity / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / small ribosomal subunit / GDP binding / cytosolic small ribosomal subunit / regulation of translation / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / GTPase activity / response to antibiotic / GTP binding / zinc ion binding / membrane / metal ion binding / cytosol
Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S20 / Ribosomal protein S12, bacterial-type / Ribosomal protein S5, C-terminal / Ribosomal protein S15, bacterial-type / Ribosome biogenesis GTPase RsgA / K Homology domain / K Homology domain, type 2 / RNA-binding S4 domain / Ribosomal protein S19/S15 ...Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S20 / Ribosomal protein S12, bacterial-type / Ribosomal protein S5, C-terminal / Ribosomal protein S15, bacterial-type / Ribosome biogenesis GTPase RsgA / K Homology domain / K Homology domain, type 2 / RNA-binding S4 domain / Ribosomal protein S19/S15 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S11 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S13 / Ribosomal protein S2 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S5 / Ribosomal protein S18, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5, N-terminal / Ribosomal protein S5, bacterial-type / Nucleic acid-binding, OB-fold / Ribosomal protein S13-like, H2TH / RsgA GTPase domain / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / Ribosomal protein S12/S23 / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S14 / Ribosomal protein S9 / Ribosomal protein S14, conserved site / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S6 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S8 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S19 conserved site / Ribosomal protein S15 / Ribosomal protein S6 / Ribosomal protein S16 / Ribosomal protein S17/S11 / Ribosomal protein S5/S7 / Ribosomal protein S3, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein S11, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6, conserved site / Ribosomal protein S13, conserved site
30S ribosomal protein S2 / 30S ribosomal protein S13 / 30S ribosomal protein S16 / 30S ribosomal protein S19 / 30S ribosomal protein S20 / 30S ribosomal protein S14 / 30S ribosomal protein S3 / 30S ribosomal protein S4 / 30S ribosomal protein S5 / 30S ribosomal protein S5 ...30S ribosomal protein S2 / 30S ribosomal protein S13 / 30S ribosomal protein S16 / 30S ribosomal protein S19 / 30S ribosomal protein S20 / 30S ribosomal protein S14 / 30S ribosomal protein S3 / 30S ribosomal protein S4 / 30S ribosomal protein S5 / 30S ribosomal protein S5 / 30S ribosomal protein S15 / 30S ribosomal protein S10 / Small ribosomal subunit biogenesis GTPase RsgA / 30S ribosomal protein S13 / 30S ribosomal protein S19 / 30S ribosomal protein S7 / 30S ribosomal protein S6 / 30S ribosomal protein S18 / 30S ribosomal protein S16 / 30S ribosomal protein S12 / 30S ribosomal protein S10 / 30S ribosomal protein S3 / 30S ribosomal protein S17 / 30S ribosomal protein S14 / 30S ribosomal protein S8 / 30S ribosomal protein S11 / 30S ribosomal protein S4 / 30S ribosomal protein S9 / 30S ribosomal protein S2 / 30S ribosomal protein S20 / 30S ribosomal protein S15
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsRazi A / Guarne A / Ortega J
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-82930 Canada
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly.
Authors: Aida Razi / Alba Guarné / Joaquin Ortega /
Abstract: Recent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with ...Recent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with high affinity. To determine the function and mechanisms of YjeQ in the context of the mature subunit, we determined the cryo-EM structure of the fully assembled 30S subunit in complex with YjeQ at 5.8-Å resolution. We found that binding of YjeQ stabilizes helix 44 into a conformation similar to that adopted by the subunit during proofreading. This finding indicates that, along with acting as an assembly factor, YjeQ has a role as a checkpoint protein, consisting of testing the proofreading ability of the 30S subunit. The structure also informs the mechanism by which YjeQ implements the release from the 30S subunit of a second assembly factor, called RbfA. Finally, it reveals how the 30S subunit stimulates YjeQ GTPase activity and leads to release of the protein. Checkpoint functions have been described for eukaryotic ribosome assembly factors; however, this work describes an example of a bacterial assembly factor that tests a specific translation mechanism of the 30S subunit.
Validation ReportPDB-ID: 5uz4

SummaryFull reportAbout validation report
History
DepositionFeb 24, 2017-
Header (metadata) releaseApr 19, 2017-
Map releaseApr 19, 2017-
UpdateJan 15, 2020-
Current statusJan 15, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0309
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0309
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5uz4
  • Surface level: 0.0309
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8621.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 220 pix.
= 319. Å
1.45 Å/pix.
x 220 pix.
= 319. Å
1.45 Å/pix.
x 220 pix.
= 319. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density
Contour LevelBy AUTHOR: 0.0309 / Movie #1: 0.0309
Minimum - Maximum-0.034293998 - 0.09952094
Average (Standard dev.)0.0011337413 (±0.0060786973)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 319.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z319.000319.000319.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0340.1000.001

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Supplemental data

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Sample components

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Entire Structure of the 30S subunit in complex with YjeQ GTPase

EntireName: Structure of the 30S subunit in complex with YjeQ GTPase
Number of components: 24

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Component #1: protein, Structure of the 30S subunit in complex with YjeQ GTPase

ProteinName: Structure of the 30S subunit in complex with YjeQ GTPase
Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Component #2: nucleic-acid, 16S RIBOSOMAL RNA

nucleic acidName: 16S RIBOSOMAL RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: GAAGAGUUUG AUCAUGGCUC AGAUUGAACG CUGGCGGCAG GCCUAACACA UGCAAGUCGA ACGGUAACAG GAAGAAGCUU GCUUCUUUGC UGACGAGUGG CGGACGGGUG AGUAAUGUCU GGGAAACUGC CUGAUGGAGG GGGAUAACUA CUGGAAACGG UAGCUAAUAC ...Sequence:
GAAGAGUUUG AUCAUGGCUC AGAUUGAACG CUGGCGGCAG GCCUAACACA UGCAAGUCGA ACGGUAACAG GAAGAAGCUU GCUUCUUUGC UGACGAGUGG CGGACGGGUG AGUAAUGUCU GGGAAACUGC CUGAUGGAGG GGGAUAACUA CUGGAAACGG UAGCUAAUAC CGCAUAACGU CGCAAGACCA AAGAGGGGGA CCUUCGGGCC UCUUGCCAUC GGAUGUGCCC AGAUGGGAUU AGCUAGUAGG UGGGGUAACG GCUCACCUAG GCGACGAUCC CUAGCUGGUC UGAGAGGAUG ACCAGCCACA CUGGAACUGA GACACGGUCC AGACUCCUAC GGGAGGCAGC AGUGGGGAAU AUUGCACAAU GGGCGCAAGC CUGAUGCAGC CAUGCCGCGU GUAUGAAGAA GGCCUUCGGG UUGUAAAGUA CUUUCAGCGG GGAGGAAGGG AGUAAAGUUA AUACCUUUGC UCAUUGACGU UACCCGCAGA AGAAGCACCG GCUAACUCCG UGCCAGCAGC CGCGGUAAUA CGGAGGGUGC AAGCGUUAAU CGGAAUUACU GGGCGUAAAG CGCACGCAGG CGGUUUGUUA AGUCAGAUGU GAAAUCCCCG GGCUCAACCU GGGAACUGCA UCUGAUACUA GCAAGCUUGA GUCUCGUAGA GGGGGGUAGA AUUCCAGGUG UAGCGGUGAA AUGCGUAGAG AUCUGGAGGA AUACCGGUGG CGAAGGCGGC CCCCUGGACG AAGACUGACG CUCAGGUGCG AAAGCGUGGG GAGCAAACAG GAUUAGAUAC CCUGGUAGUC CACGCCGUAA ACGAUGUCGA CUUGGAGGUU GUGCCCUUGA GGCGUGGCUU CCGGAGCUAA CGCGUUAAGU CGACCGCCUG GGGAGUACGG CCGCAAGGUU AAAACUCAAA UGAAUUGACG GGGGCCCGCA CAAGCGGUGG AGCAUGUGGU UUAAUUCGAU GCAACGCGAA GAACCUUACC UGGUCUUGAC AUCCACGGAA GUUUUCAGAG AUGAGAAUGU GCCUUCGGGA ACCGUGAGAC AGGUGCUGCA UGGCUGUCGU CAGCUCGUGU UGUGAAAUGU UGGGUUAAGU CCCGCAACGA GCGCAACCCU UAUCCUUUGU UGCCAGCGGU CCGGCCGGGA ACUCAAAGGA GACUGCCAGU GAUAAACUGG AGGAAGGUGG GGAUGACGUC AAGUCAUCAU GGCCCUUACG ACCAGGGCUA CACACGUGCU ACAAUGGCGC AUACAAAGAG AAGCGACCUC GCGAGAGCAA GCGGACCUCA UAAAGUGCGU CGUAGUCCGG AUUGGAGUCU GCAACUCGAC UCCAUGAAGU CGGAAUCGCU AGUAAUCGUG GAUCAGAAUG CCACGGUGAA UACGUUCCCG GGCCUUGUAC ACACCGCCCG UCACACCAUG GGAGUGGGUU GCAAAAGAAG UAGGUAGCUU AACCUUCGGG AGGGCGCUUA CCACUUUGUG AUUCAUGACU GGGGUGAAGU CGUAACAAGG UAACCGUAGG GGAACCUGCG GUUGGAU
MassTheoretical: 494.971188 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #3: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.031316 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #4: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.514199 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #5: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.629398 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #6: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.211058 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #7: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.055156 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #8: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.146557 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #9: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.88627 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #10: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.755597 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #11: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.870975 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #12: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.768157 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #13: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.128467 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #14: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.60656 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #15: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.319882 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #16: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.207572 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #17: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.724491 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #18: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.005472 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #19: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.455355 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #20: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.708464 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #21: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.78167 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #22: protein, Small ribosomal subunit biogenesis GTPase RsgA

ProteinName: Small ribosomal subunit biogenesis GTPase RsgA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.345172 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #23: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #24: ligand, 3'-O-(N-methylanthraniloyl)-beta:gamma-imidoguanosine-5'-...

LigandName: 3'-O-(N-methylanthraniloyl)-beta:gamma-imidoguanosine-5'-triphosphate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.655343 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 25000.0 X (nominal), 34482.0 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 3000.0 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 130462
3D reconstructionResolution: 5.8 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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