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- PDB-5x8t: Structure of the 50S large subunit of chloroplast ribosome from s... -

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Entry
Database: PDB / ID: 5x8t
TitleStructure of the 50S large subunit of chloroplast ribosome from spinach
Components
  • (50S ribosomal protein ...) x 18
  • 23S rRNA23S ribosomal RNA
  • 4.8S rRNA
  • 5S rRNA5S ribosomal RNA
  • protein L15
  • protein L17
  • protein L18
  • protein L27
  • protein L28
  • protein L29
  • protein L3
  • protein L6
  • protein L9
  • protein cL37
  • protein cL38
KeywordsRIBOSOME / Cryo-EM / chloroplast ribosome
Function / homology
Function and homology information


plastid translation / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast / DNA-templated transcription termination / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit ...plastid translation / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast / DNA-templated transcription termination / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding
Similarity search - Function
Ribosomal protein L28/L24 / Ribosomal protein L6, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L24e; Chain: T; ...Ribosomal protein L28/L24 / Ribosomal protein L6, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L24e; Chain: T; / Ribosomal protein L6 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Ribosomal Protein L22; Chain A / Aldehyde Oxidoreductase; domain 3 / Rubrerythrin, domain 2 / RRM (RNA recognition motif) domain / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Single Sheet / Nucleic acid-binding proteins / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL31c ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL31c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein cL38 / Large ribosomal subunit protein bL28c / Large ribosomal subunit protein bL17c / Large ribosomal subunit protein bL9c / Large ribosomal subunit protein cL37 alpha / Large ribosomal subunit protein uL4c / Large ribosomal subunit protein uL2cz/uL2cy / Large ribosomal subunit protein uL22c / Large ribosomal subunit protein uL14c / Large ribosomal subunit protein bL36c / Large ribosomal subunit protein uL13c / Large ribosomal subunit protein uL16c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein bL35c / Large ribosomal subunit protein bL21c / Large ribosomal subunit protein uL24c / Large ribosomal subunit protein cL37 alpha / Large ribosomal subunit protein bL20c / Large ribosomal subunit protein bL32c / Large ribosomal subunit protein bL33c / Large ribosomal subunit protein bL9c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL5c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein bL17c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL34c / Large ribosomal subunit protein bL28c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein bL31c / Large ribosomal subunit protein cL38 / Large ribosomal subunit protein bL19c / Large ribosomal subunit protein uL23c
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsAhmed, T. / Shi, J. / Bhushan, S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
MOEAcRF Tier 1, 2014-T1-001-019 (RG32/14) Singapore
CitationJournal: Nucleic Acids Res / Year: 2017
Title: Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation.
Authors: Tofayel Ahmed / Jian Shi / Shashi Bhushan /
Abstract: Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, ...Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, cS23, bTHXc, cL37 and cL38) which have been suggested to play important regulatory roles in translation. However, their exact locations on the chloroplast ribosome remain elusive due to lack of a high-resolution structure, hindering our progress to understand their possible roles. Here we present a cryo-EM structure of the 70S chloroplast ribosome from spinach resolved to 3.4 Å and focus our discussion mainly on the architecture of the 30S small subunit (SSU) which is resolved to 3.7 Å. cS22 localizes at the SSU foot where it seems to compensate for the deletions in 16S rRNA. The mRNA exit site is highly remodeled due to the presence of cS23 suggesting an alternative mode of translation initiation. bTHXc is positioned at the SSU head and appears to stabilize the intersubunit bridge B1b during thermal fluctuations. The translation factor plastid pY binds to the SSU on the intersubunit side and interacts with the conserved nucleotide bases involved in decoding. Most of the intersubunit bridges are conserved compared to the bacteria, except for a new bridge involving uL2c and bS6c.
History
DepositionMar 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jun 6, 2018Group: Data collection / Category: em_image_scans / em_software
Item: _em_image_scans.dimension_height / _em_image_scans.dimension_width / _em_software.name
Revision 1.4Oct 16, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.5Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
1: 50S ribosomal protein L32, chloroplastic
2: 50S ribosomal protein L33, chloroplastic
3: 50S ribosomal protein L34, chloroplastic
4: 50S ribosomal protein L35, chloroplastic
5: 50S ribosomal protein L36, chloroplastic
6: protein cL37
7: protein cL38
B: 5S rRNA
C: 50S ribosomal protein L2, chloroplastic
D: protein L3
E: 50S ribosomal protein L4, chloroplastic
F: 50S ribosomal protein L5, chloroplastic
G: protein L6
H: protein L9
K: 50S ribosomal protein L13, chloroplastic
L: 50S ribosomal protein L14, chloroplastic
M: protein L15
N: 50S ribosomal protein L16, chloroplastic
O: protein L17
P: protein L18
Q: 50S ribosomal protein L19, chloroplastic
R: 50S ribosomal protein L20, chloroplastic
S: 50S ribosomal protein L21, chloroplastic
T: 50S ribosomal protein L22, chloroplastic
U: 50S ribosomal protein L23, chloroplastic
V: 50S ribosomal protein L24, chloroplastic
W: 4.8S rRNA
X: protein L27
Y: protein L28
Z: protein L29
A: 23S rRNA
0: 50S ribosomal protein L31


Theoretical massNumber of molelcules
Total (without water)1,446,40332
Polymers1,446,40332
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area179410 Å2
ΔGint-1550 kcal/mol
Surface area501190 Å2

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Components

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50S ribosomal protein ... , 18 types, 18 molecules 12345CEFKLNQRSTUV0

#1: Protein 50S ribosomal protein L32, chloroplastic / Ribosome


Mass: 6519.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28804
#2: Protein 50S ribosomal protein L33, chloroplastic / Ribosome


Mass: 7536.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28805
#3: Protein 50S ribosomal protein L34, chloroplastic / Ribosome / CL34


Mass: 6789.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82244
#4: Protein 50S ribosomal protein L35, chloroplastic / Ribosome / CL35


Mass: 8459.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P23326
#5: Protein/peptide 50S ribosomal protein L36, chloroplastic / Ribosome


Mass: 4414.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12230
#9: Protein 50S ribosomal protein L2, chloroplastic / Ribosome / Ribosomal protein CS-L4


Mass: 29722.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06509
#11: Protein 50S ribosomal protein L4, chloroplastic / Ribosome / R-protein L4


Mass: 27202.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: O49937
#12: Protein 50S ribosomal protein L5, chloroplastic / Ribosome


Mass: 24248.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82192
#15: Protein 50S ribosomal protein L13, chloroplastic / Ribosome / CL13


Mass: 22774.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12629
#16: Protein 50S ribosomal protein L14, chloroplastic / Ribosome / Ribosomal protein CS-L29


Mass: 13484.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09596
#18: Protein 50S ribosomal protein L16, chloroplastic / Ribosome / Ribosomal protein CS-L24


Mass: 15328.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P17353
#21: Protein 50S ribosomal protein L19, chloroplastic / Ribosome / CL19


Mass: 17597.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82413
#22: Protein 50S ribosomal protein L20, chloroplastic / Ribosome


Mass: 15594.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28803
#23: Protein 50S ribosomal protein L21, chloroplastic / Ribosome / CL21 / CS-L7


Mass: 22793.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P24613
#24: Protein 50S ribosomal protein L22, chloroplastic / Ribosome / Ribosomal protein CS-L13


Mass: 23292.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09594
#25: Protein 50S ribosomal protein L23, chloroplastic / Ribosome / PRPL23


Mass: 13575.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9LWB5
#26: Protein 50S ribosomal protein L24, chloroplastic / Ribosome / CL24


Mass: 16552.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P27683
#32: Protein 50S ribosomal protein L31 /


Mass: 10801.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R0R6, UniProt: P82249*PLUS

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Protein , 11 types, 11 molecules 67DGHMOPXYZ

#6: Protein protein cL37


Mass: 15694.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9S2M7, UniProt: P27684*PLUS
#7: Protein protein cL38


Mass: 12080.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RCH6, UniProt: P82411*PLUS
#10: Protein protein L3


Mass: 24117.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QEC7, UniProt: P82191*PLUS
#13: Protein protein L6


Mass: 20263.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R4N9, UniProt: P82193*PLUS
#14: Protein protein L9


Mass: 17669.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RQ91, UniProt: P82180*PLUS
#17: Protein protein L15


Mass: 20680.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QHT0, UniProt: P22798*PLUS
#19: Protein protein L17


Mass: 13466.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RLJ4, UniProt: P82194*PLUS
#20: Protein protein L18


Mass: 13801.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QQ60, UniProt: P82195*PLUS
#28: Protein protein L27


Mass: 15326.538 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R4I2, UniProt: P82190*PLUS
#29: Protein protein L28


Mass: 9016.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RD02, UniProt: P82245*PLUS
#30: Protein protein L29


Mass: 12903.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R7W8, UniProt: P82248*PLUS

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RNA chain , 3 types, 3 molecules BWA

#8: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 39014.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
#27: RNA chain 4.8S rRNA


Mass: 34334.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 12299
#31: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 911344.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 7636084

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 50S large subunit of chloroplast ribosome from spinach
Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightValue: 1.7 MDa / Experimental value: NO
Source (natural)Organism: Spinacia oleracea (spinach)
Buffer solutionpH: 7.6
Details: 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
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Calibrated magnification: 133333 X / Nominal defocus max: 3700 nm / Nominal defocus min: 400 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 3700 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3161
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 25 / Used frames/image: 1-25

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Processing

EM software
IDNameCategory
1EMAN2particle selection
4CTFFIND3CTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 187946
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81305 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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