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- EMDB-0643: 30S initiation complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0643
Title30S initiation complex
Map data
Sample70S elongation competent ribosome
  • (Translation initiation factor IF- ...) x 2
  • (nucleic-acidNucleic acid) x 3
  • (30S ribosomal protein ...) x 20
Function / homology
Function and homology information


translation initiation factor activity / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / ribosome / rRNA binding ...translation initiation factor activity / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / GTPase activity / mRNA binding / GTP binding / cytosol / cytoplasm
Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / 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 S8 superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3 signature. ...Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / 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 S8 superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3 signature. / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S18 superfamily / Translation initiation factor IF-2, domain 3 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S19, superfamily / Elongation factor Tu GTP binding domain / Ribosomal protein S16, 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 S7, conserved site / Translation initiation factor IF- 2, domain 3 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S4/S9 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S21, conserved site / Ribosomal protein S8 signature. / Ribosomal protein S5, C-terminal domain / Translation initiation factor IF-2, N-terminal region / KH domain / Bacterial translation initiation factor IF-2 associated region / Translation-initiation factor 2 / Ribosomal protein S7 signature. / Ribosomal protein S11 signature. / S4 domain / Ribosomal protein S12 signature. / Ribosomal protein S17 signature. / Ribosomal protein S18 signature. / Ribosomal protein S19 signature. / Ribosomal protein S9 signature. / Ribosomal protein S10 signature. / Ribosomal protein S20 / Ribosomal protein S6 / Ribosomal protein S12/S23 / Ribosomal protein S5, N-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein S19 / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S2 / Ribosomal protein S10p/S20e / Ribosomal protein S21 / Ribosomal protein S17 / Ribosomal protein S9/S16 / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein S13/S18 / Ribosomal protein S16 / Ribosomal protein S18 / Ribosomal protein S3, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S14 / Ribosomal protein S6 / Ribosomal protein S15 / Ribosomal protein S8 / Ribosomal protein S9 / Transcription factor, GTP-binding domain / Ribosomal protein S5 / Ribosomal protein S3, C-terminal / Ribosomal protein S17/S11 / Ribosomal protein S18 / Ribosomal protein S10 / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S21 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S16 / Ribosomal protein S5/S7 / Ribosomal protein S14, conserved site / Initiation factor 2 signature. / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / S4 RNA-binding domain profile. / S5 double stranded RNA-binding domain profile. / Type-2 KH domain profile. / Ribosomal protein S13 family profile. / Ribosomal protein S21 signature. / Ribosomal protein S6 signature.
30S ribosomal protein S19 / 30S ribosomal protein S2 / 30S ribosomal protein S9 / 30S ribosomal protein S20 / 30S ribosomal protein S7 / 30S ribosomal protein S6 / 30S ribosomal protein S11 / 30S ribosomal protein S4 / 30S ribosomal protein S18 / 30S ribosomal protein S21 ...30S ribosomal protein S19 / 30S ribosomal protein S2 / 30S ribosomal protein S9 / 30S ribosomal protein S20 / 30S ribosomal protein S7 / 30S ribosomal protein S6 / 30S ribosomal protein S11 / 30S ribosomal protein S4 / 30S ribosomal protein S18 / 30S ribosomal protein S21 / 30S ribosomal protein S8 / 30S ribosomal protein S15 / 30S ribosomal protein S10 / 30S ribosomal protein S16 / 30S ribosomal protein S5 / 30S ribosomal protein S3 / 30S ribosomal protein S13 / 30S ribosomal protein S14 / 30S ribosomal protein S17 / Translation initiation factor IF-2 / 30S ribosomal protein S12
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsFrank J / Gonzalez Jr RL / kaledhonkar S / Fu Z / Caban K / Li W / Chen B / Sun M
CitationJournal: Nature / Year: 2019
Title: Late steps in bacterial translation initiation visualized using time-resolved cryo-EM.
Authors: Sandip Kaledhonkar / Ziao Fu / Kelvin Caban / Wen Li / Bo Chen / Ming Sun / Ruben L Gonzalez / Joachim Frank /
Abstract: The initiation of bacterial translation involves the tightly regulated joining of the 50S ribosomal subunit to an initiator transfer RNA (fMet-tRNA)-containing 30S ribosomal initiation complex to ...The initiation of bacterial translation involves the tightly regulated joining of the 50S ribosomal subunit to an initiator transfer RNA (fMet-tRNA)-containing 30S ribosomal initiation complex to form a 70S initiation complex, which subsequently matures into a 70S elongation-competent complex. Rapid and accurate formation of the 70S initiation complex is promoted by initiation factors, which must dissociate from the 30S initiation complex before the resulting 70S elongation-competent complex can begin the elongation of translation. Although comparisons of the structures of the 30S and 70S initiation complexes have revealed that the ribosome, initiation factors and fMet-tRNA can acquire different conformations in these complexes, the timing of conformational changes during formation of the 70S initiation complex, the structures of any intermediates formed during these rearrangements, and the contributions that these dynamics might make to the mechanism and regulation of initiation remain unknown. Moreover, the absence of a structure of the 70S elongation-competent complex formed via an initiation-factor-catalysed reaction has precluded an understanding of the rearrangements to the ribosome, initiation factors and fMet-tRNA that occur during maturation of a 70S initiation complex into a 70S elongation-competent complex. Here, using time-resolved cryogenic electron microscopy, we report the near-atomic-resolution view of how a time-ordered series of conformational changes drive and regulate subunit joining, initiation factor dissociation and fMet-tRNA positioning during formation of the 70S elongation-competent complex. Our results demonstrate the power of time-resolved cryogenic electron microscopy to determine how a time-ordered series of conformational changes contribute to the mechanism and regulation of one of the most fundamental processes in biology.
Validation ReportPDB-ID: 6o7k

SummaryFull reportAbout validation report
DateDeposition: Mar 8, 2019 / Header (metadata) release: May 29, 2019 / Map release: May 29, 2019 / Update: May 29, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
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  • Surface view colored by height
  • Surface level: 0.04
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  • Surface view with fitted model
  • Atomic models: : PDB-6o7k
  • Surface level: 0.04
  • 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_0643.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 256 pix.
= 424.96 Å
1.66 Å/pix.
x 256 pix.
= 424.96 Å
1.66 Å/pix.
x 256 pix.
= 424.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.04
Minimum - Maximum-0.067953154 - 0.23054652
Average (Standard dev.)0.0008448038 (±0.008188761)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.661.661.66
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z424.960424.960424.960
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0680.2310.001

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Supplemental data

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Sample components

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Entire 70S elongation competent ribosome

EntireName: 70S elongation competent ribosome / Number of components: 26

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Component #1: protein, 70S elongation competent ribosome

ProteinName: 70S elongation competent ribosome / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Component #2: protein, Translation initiation factor IF-1

ProteinName: Translation initiation factor IF-1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.116468 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #3: protein, Translation initiation factor IF-2

ProteinName: Translation initiation factor IF-2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.866508 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #4: nucleic-acid, 16S

nucleic acidName: 16S16S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUCU UUGCUGACGA GUGGCGGACG GGUGAGUAAU GUCUGGGAAA CUGCCUGAUG GAGGGGGAUA ACUACUGGAA ACGGUAGCUA AUACCGCAUA ACGUCGCAAG ACCAAAGAGG GGGACCUUCG GGCCUCUUGC CAUCGGAUGU GCCCAGAUGG GAUUAGCUAG UAGGUGGGGU AACGGCUCAC CUAGGCGACG AUCCCUAGCU GGUCUGAGAG GAUGACCAGC CACACUGGAA CUGAGACACG GUCCAGACUC CUACGGGAGG CAGCAGUGGG GAAUAUUGCA CAAUGGGCGC AAGCCUGAUG CAGCCAUGCC GCGUGUAUGA AGAAGGCCUU CGGGUUGUAA AGUACUUUCA GCGGGGAGGA AGGGAGUAAA GUUAAUACCU UUGCUCAUUG ACGUUACCCG CAGAAGAAGC ACCGGCUAAC UCCGUGCCAG CAGCCGCGGU AAUACGGAGG GUGCAAGCGU UAAUCGGAAU UACUGGGCGU AAAGCGCACG CAGGCGGUUU GUUAAGUCAG AUGUGAAAUC CCCGGGCUCA ACCUGGGAAC UGCAUCUGAU ACUGGCAAGC UUGAGUCUCG UAGAGGGGGG UAGAAUUCCA GGUGUAGCGG UGAAAUGCGU AGAGAUCUGG AGGAAUACCG GUGGCGAAGG CGGCCCCCUG GACGAAGACU GACGCUCAGG UGCGAAAGCG UGGGGAGCAA ACAGGAUUAG AUACCCUGGU AGUCCACGCC GUAAACGAUG UCGACUUGGA GGUUGUGCCC UUGAGGCGUG GCUUCCGGAG CUAACGCGUU AAGUCGACCG CCUGGGGAGU ACGGCCGCAA GGUUAAAACU CAAAUGAAUU GACGGGGGCC CGCACAAGCG GUGGAGCAUG UGGUUUAAUU CGAUGCAACG CGAAGAACCU UACCUGGUCU UGACAUCCAC GGAAGUUUUC AGAGAUGAGA AUGUGCCUUC GGGAACCGUG AGACAGGUGC UGCAUGGCUG UCGUCAGCUC GUGUUGUGAA AUGUUGGGUU AAGUCCCGCA ACGAGCGCAA CCCUUAUCCU UUGUUGCCAG CGGUCCGGCC GGGAACUCAA AGGAGACUGC CAGUGAUAAA CUGGAGGAAG GUGGGGAUGA CGUCAAGUCA UCAUGGCCCU UACGACCAGG GCUACACACG UGCUACAAUG GCGCAUACAA AGAGAAGCGA CCUCGCGAGA GCAAGCGGAC CUCAUAAAGU GCGUCGUAGU CCGGAUUGGA GUCUGCAACU CGACUCCAUG AAGUCGGAAU CGCUAGUAAU CGUGGAUCAG AAUGCCACGG UGAAUACGUU CCCGGGCCUU GUACACACCG CCCGUCACAC CAUGGGAGUG GGUUGCAAAA GAAGUAGGUA GCUUAACCUU CGGGAGGGCG CUUACCACUU UGUGAUUCAU GACUGGGGUG AAGUCGUAAC AAGGUAACCG UAGGGGAACC UGCGGUUGGA UCACCUCCU
MassTheoretical: 498.725406 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #5: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.263946 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #6: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.196988 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #7: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.4872 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #8: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.636961 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #9: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.625753 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #10: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.48939 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #11: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.159621 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #12: 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 #13: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.466477 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #14: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.057626 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #15: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.253943 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #16: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.50619 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #17: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.067081 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #18: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.078785 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #19: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.383002 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #20: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.804282 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #21: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.669371 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #22: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.861523 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #23: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.015361 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #24: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.554882 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #25: nucleic-acid, tRNA

nucleic acidName: tRNATransfer RNA / 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 #26: nucleic-acid, mRNA

nucleic acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAUAUG
MassTheoretical: 1.900198 kDa
SourceSpecies: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/Å2 / Illumination mode: OTHER
LensImaging mode: DARK FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 86367
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 2AVY
Output model

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