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- EMDB-6710: Structure of the 30S small subunit of chloroplast ribosome from s... -

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Entry
Database: EMDB / ID: 6710
TitleStructure of the 30S small subunit of chloroplast ribosome from spinach
Sample30S small subunit of chloroplast ribosome from spinach
SourceSpinacia oleracea / plant / spinach / ホウレンソウ
Map data
Methodsingle particle reconstruction, at 3.7 Å resolution
AuthorsAhmed T / Shi J
CitationNucleic Acids Res., 2017, 45, 8581-8595

Nucleic Acids Res., 2017, 45, 8581-8595 Yorodumi Papers
Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation.
Tofayel Ahmed / Jian Shi / Shashi Bhushan

Validation ReportPDB-ID: 5x8r

SummaryFull reportAbout validation report
DateDeposition: Mar 3, 2017 / Header (metadata) release: Jun 7, 2017 / Map release: Jun 7, 2017 / Last update: Sep 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-5x8r
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_6710.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.05 Å/pix.
= 403.2 Å
384 pix
1.05 Å/pix.
= 403.2 Å
384 pix
1.05 Å/pix.
= 403.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.17213282 - 0.3157689
Average (Standard dev.)0.0006205938 (0.008562695)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin000
Limit383383383
Spacing384384384
CellA=B=C: 403.19998 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z403.200403.200403.200
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-0.1720.3160.001

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Supplemental data

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Sample components

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Entire 30S small subunit of chloroplast ribosome from spinach

EntireName: 30S small subunit of chloroplast ribosome from spinach
Number of components: 27
MassTheoretical: 1.7 MDa

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Component #1: protein, 30S small subunit of chloroplast ribosome from spinach

ProteinName: 30S small subunit of chloroplast ribosome from spinach
Recombinant expression: No
MassTheoretical: 1.7 MDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #2: protein, 30S ribosomal protein S2, chloroplastic

ProteinName: 30S ribosomal protein S2, chloroplastic / Recombinant expression: No
MassTheoretical: 26.736141 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #3: protein, 30S ribosomal protein S3, chloroplastic

ProteinName: 30S ribosomal protein S3, chloroplastic / Recombinant expression: No
MassTheoretical: 24.965156 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #4: protein, 30S ribosomal protein S5, chloroplastic

ProteinName: 30S ribosomal protein S5, chloroplastic / Recombinant expression: No
MassTheoretical: 27.69658 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #5: protein, 30S ribosomal protein S6 alpha, chloroplastic

ProteinName: 30S ribosomal protein S6 alpha, chloroplastic / Recombinant expression: No
MassTheoretical: 16.341423 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #6: protein, 30S ribosomal protein S7, chloroplastic

ProteinName: 30S ribosomal protein S7, chloroplastic / Recombinant expression: No
MassTheoretical: 17.378309 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #7: protein, 30S ribosomal protein S8, chloroplastic

ProteinName: 30S ribosomal protein S8, chloroplastic / Recombinant expression: No
MassTheoretical: 15.527256 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #8: protein, 30S ribosomal protein S9, chloroplastic

ProteinName: 30S ribosomal protein S9, chloroplastic / Recombinant expression: No
MassTheoretical: 17.092791 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #9: protein, protein S10

ProteinName: protein S10 / Recombinant expression: No
MassTheoretical: 13.882167 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #10: protein, 30S ribosomal protein S11, chloroplastic

ProteinName: 30S ribosomal protein S11, chloroplastic / Recombinant expression: No
MassTheoretical: 14.927551 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #11: protein, 30S ribosomal protein S12, chloroplastic

ProteinName: 30S ribosomal protein S12, chloroplastic / Recombinant expression: No
MassTheoretical: 13.794261 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #12: protein, 30S ribosomal protein S13, chloroplastic

ProteinName: 30S ribosomal protein S13, chloroplastic / Recombinant expression: No
MassTheoretical: 14.418822 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #13: protein, 30S ribosomal protein S15, chloroplastic

ProteinName: 30S ribosomal protein S15, chloroplastic / Recombinant expression: No
MassTheoretical: 10.778763 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #14: protein, 30S ribosomal protein S16, chloroplastic

ProteinName: 30S ribosomal protein S16, chloroplastic / Recombinant expression: No
MassTheoretical: 10.454237 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #15: protein, protein S17

ProteinName: protein S17 / Recombinant expression: No
MassTheoretical: 12.195099 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #16: protein, 30S ribosomal protein S18, chloroplastic

ProteinName: 30S ribosomal protein S18, chloroplastic / Recombinant expression: No
MassTheoretical: 12.079137 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #17: protein, 30S ribosomal protein S19 alpha, chloroplastic

ProteinName: 30S ribosomal protein S19 alpha, chloroplastic / Recombinant expression: No
MassTheoretical: 10.6325 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #18: protein, protein S20

ProteinName: protein S20 / Recombinant expression: No
MassTheoretical: 12.17809 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #19: protein, protein S21

ProteinName: protein S21 / Recombinant expression: No
MassTheoretical: 16.096171 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #20: protein, protein plastid pY

ProteinName: protein plastid pY / Recombinant expression: No
MassTheoretical: 26.85133 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #21: nucleic-acid, 16S rRNA

Nucleic-acidName: 16S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UCUCAUGGAG AGUUCGAUCC UGGCUCAGGA UGAACGCUGG CGGCAUGCUU AACACAUGCA AGUCGGACGG GAAGUGGUGU UUCCAGUGGC GGACGGGUGA GUAACGCGUA AGAACCUGCC CUUGGGAGGG GAACAACAGC UGGAAACGGC UGCUAAUACC CCGUAGGCUG AGAAGCAAAA GGAGGAAUCC GCCCGAGGAG GGGCUCGCGU CUGAUUAGCU AGUUGGUGAG GUAAUAGCUU ACCAAGGCGA UGAUCAGUAG CUGGUCCGAG AGGAUGAUCA GCCACACUGG GACUGAGACA CGGCCCAGAC UCCUACGGGA GGCAGCAGUG GGGAAUUUUC CGCAAUGGGC GAAAGCCUGA CGGAGCAAUG CCGCGUGGAG GCAGAAGGCC CACGGGUCGU GAACUUCUUU UCCCGGAGAA GAAGCAAUGA CGGUAUCCGG GGAAUAAGCA UCGGCUAACU CUGUGCCAGC AGCCGCGGUA AGACAGAGGA UGCAAGCGUU AUCCGGAAUG AUUGGGCGUA AAGCGUCUGU AGGUGGCUUU UUAAGUCCGC CGUCAAAUCC CAGGGCUCAA CCCUGGACAG GCGGUGGAAA CUACCAAGCU GGAGUACGGU AGGGGCAGAG GGAAUUUCCG GUGGAGCGGU GAAAUGCGUA GAGAUCGGAA AGAACACCAA CGGCGAAAGC ACUCUGCUGG GCCGACACUG ACACUGAGAG ACGAAAGCUA GGGGAGCGAA UGGGAUUAGA UACCCCAGUA GUCCUAGCCG UAAACGAUGG AUACUAGGCG CUGUGCGUAU CGACCCGUGC AGUGUUGUAG CUAACGCGUU AAGUAUCCCG CCUGGGGAGU ACGUUCGCAA GAAUGAAACU CAAAGGAAUU GACGGGGGCC CGCACAAGCG GUGGAGCAUG UGGUUUAAUU CGAUGCAAAG CGAAGAACCU UACCAGGGCU UGACAUGCCG CGAAUCCUCU UGAAAGAGAG GGGUGCCUUC GGGAACGCGG ACACAGGUGG UGCAUGGCUG UCGUCAGCUC GUGCCGUAAG GUGUUGGGUU AAGUCCCGCA ACGAGCGCAA CCCUCGUGUU UAGUUGCCAA CGUUGAGUUU GGAACCCUGA ACAGACUGCC GGUGAUAAGC CGGAGGAAGG UGAGGAUGAC GUCAAGUCAU CAUGCCCCUU AUGCCCUGGG CGACACACGU GCUACAAUGG CCGGGACAAA GGGUCGCGAU CCCGCGAGGG UGAGCUAACC CCAAAAACCC GUCCUCAGUU CGGAUUGCAG GCUGCAACUC GCCUGCAUGA AGCCGGAAUC GCUAGUAAUC GCCGGUCAGC CAUACGGCGG UGAAUUCGUU CCCGGGCCUU GUACACACCG CCCGUCACAC UAUGGGAGCU GGCCAUGCCC GAAGUCGUUA CCUUAACCGC AAGGAGGGGG AUGCCGAAGG CAGGGCUAGU GACUGGAGUG AAGUCGUAAC AAGGUAGCCG UACUGGAAGG UGCGGCUGGA UCACCUCCUU U
MassTheoretical: 483.4665 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #22: protein, protein cS23

ProteinName: protein cS23 / Recombinant expression: No
MassTheoretical: 13.808066 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #23: protein, 30S ribosomal protein S4, chloroplastic

ProteinName: 30S ribosomal protein S4, chloroplastic / Recombinant expression: No
MassTheoretical: 23.454531 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #24: protein, protein cS22

ProteinName: protein cS22 / Recombinant expression: No
MassTheoretical: 21.691145 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #25: protein, 30S ribosomal protein S14, chloroplastic

ProteinName: 30S ribosomal protein S14, chloroplastic / Recombinant expression: No
MassTheoretical: 11.809832 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #26: protein, protein bTHXc

ProteinName: protein bTHXc / Recombinant expression: No
MassTheoretical: 5.188887 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #27: protein, 30S ribosomal protein S1, chloroplastic

ProteinName: 30S ribosomal protein S1, chloroplastic / Recombinant expression: No
MassTheoretical: 40.472961 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 20 mM Tris HCl, pH 7.6, 100 mM KCl, 10 mM MgOAc, 100 mM sucrose, 7 mM 2-mercaptoethanol, 1 unit/ml RNase inhibitor, 0.1% protease inhibitor
pH: 7.6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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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: 1.5 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 75000 X (nominal), 133333 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 400 - 3700 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3161 / Sampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 81305
3D reconstructionAlgorithm: FOURIER SPACE / Software: Relion / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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