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- EMDB-3532: Cryo-EM reconstruction of the small subunit of the chloroplast ri... -

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Entry
Database: EMDB / ID: 3532
TitleCryo-EM reconstruction of the small subunit of the chloroplast ribosome
SampleChloroplast 70S ribosome
SourceSpinacia oleracea / plant / spinach / ホウレンソウ
Map dataCryo-EM reconstruction of the 30S small subunit of the chloroplast ribosome
Methodsingle particle reconstruction, at 3.6 Å resolution
AuthorsBieri P / Leibundgut M
CitationEMBO J., 2017, 36, 475-486

EMBO J., 2017, 36, 475-486 Yorodumi Papers
The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.
Philipp Bieri / Marc Leibundgut / Martin Saurer / Daniel Boehringer / Nenad Ban

Validation ReportPDB-ID: 5mmj

SummaryFull reportAbout validation report
DateDeposition: Dec 10, 2016 / Header (metadata) release: Jan 11, 2017 / Map release: Jan 11, 2017 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5mmj
  • Surface level: 0.06
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3532.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.39 Å/pix.
= 444.8 Å
320 pix
1.39 Å/pix.
= 444.8 Å
320 pix
1.39 Å/pix.
= 444.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour Level:0.06 (by author), 0.06 (movie #1):
Minimum - Maximum-0.10384296 - 0.34530732
Average (Standard dev.)0.0009308014 (0.010387902)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 444.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z444.800444.800444.800
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-0.1040.3450.001

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Supplemental data

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Sample components

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Entire Chloroplast 70S ribosome

EntireName: Chloroplast 70S ribosome / Number of components: 29
MassTheoretical: 2.4 MDa

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Component #1: protein, Chloroplast 70S ribosome

ProteinName: Chloroplast 70S ribosome / Recombinant expression: No
MassTheoretical: 2.4 MDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ
Source (natural)Organelle: chloroplast / Organ or tissue: leaf

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Component #2: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Recombinant expression: No
MassTheoretical: 14.748201 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #3: protein, plastid ribosomal protein bS1c

ProteinName: plastid ribosomal protein bS1c
Details: Residues were built as poly-alanine and deposited as UNK.
Recombinant expression: No
MassTheoretical: 14.826253 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #4: nucleic-acid, 16S ribosomal RNA

Nucleic-acidName: 16S ribosomal RNA / 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 #5: 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 #6: 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 #7: 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 #8: protein, 30S ribosomal protein S5, chloroplastic

ProteinName: 30S ribosomal protein S5, chloroplastic
Details: Residues 122-150 were built as poly-alanine and deposited as UNK.
Recombinant expression: No
MassTheoretical: 33.626363 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #9: protein, plastid ribosomal protein bS6c

ProteinName: plastid ribosomal protein bS6c / Recombinant expression: No
MassTheoretical: 23.510664 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #10: 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 #11: 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 #12: protein, plastid ribosomal protein uS9c

ProteinName: plastid ribosomal protein uS9c / Recombinant expression: No
MassTheoretical: 22.415057 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #13: protein, plastid ribosomal protein uS10c

ProteinName: plastid ribosomal protein uS10c / Recombinant expression: No
MassTheoretical: 21.440539 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #14: 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 #15: 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 #16: protein, plastid ribosomal protein uS13c

ProteinName: plastid ribosomal protein uS13c / Recombinant expression: No
MassTheoretical: 19.310641 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #17: 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 #18: 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 #19: 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 #20: protein, plastid ribosomal protein uS17c

ProteinName: plastid ribosomal protein uS17c / Recombinant expression: No
MassTheoretical: 18.151936 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #21: 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 #22: 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 #23: protein, plastid ribosomal protein bS20c

ProteinName: plastid ribosomal protein bS20c / Recombinant expression: No
MassTheoretical: 20.147291 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #24: protein, plastid ribosomal protein bS21c

ProteinName: plastid ribosomal protein bS21c / Recombinant expression: No
MassTheoretical: 20.61615 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #25: protein, 30S ribosomal protein 2, chloroplastic

ProteinName: 30S ribosomal protein 2, chloroplastic / Recombinant expression: No
MassTheoretical: 28.327863 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #26: protein, 30S ribosomal protein 3, chloroplastic

ProteinName: 30S ribosomal protein 3, chloroplastic / Recombinant expression: No
MassTheoretical: 20.31275 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #27: protein, 30S ribosomal protein S31, chloroplastic

ProteinName: 30S ribosomal protein S31, chloroplastic / Recombinant expression: No
MassTheoretical: 10.602076 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #28: protein, Ribosome-binding factor PSRP1, chloroplastic

ProteinName: Ribosome-binding factor PSRP1, chloroplastic / Recombinant expression: No
MassTheoretical: 33.799266 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #29: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 185 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.12 mg/ml / pH: 7.6
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 278 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: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 3500 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: 2796

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 127031
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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