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- PDB-9vtg: cryoEM structure of tobacco mosaic virus tRNA-like structure comp... -

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Basic information

Entry
Database: PDB / ID: 9vtg
TitlecryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 60S
Components
  • (60S ribosomal protein ...) x 34
  • (Large ribosomal subunit protein ...) x 3
  • (Ribosomal protein ...) x 3
  • 25S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • RNA (204-MER)
  • Ribosomal protein
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / tRNA-like structure / tobacco / Nicotiana benthamiana / tobacco mosaic virus / RNA structure / translation
Function / homology
Function and homology information


adaxial/abaxial pattern specification / leaf morphogenesis / response to high light intensity / response to UV-B / protein-RNA complex assembly / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly ...adaxial/abaxial pattern specification / leaf morphogenesis / response to high light intensity / response to UV-B / protein-RNA complex assembly / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / mRNA binding / RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. ...Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / metallochaperone-like domain / TRASH domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L30e signature 1. / Ribosomal L40e family / Ribosomal protein L36e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / : / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / : / Ribosomal_L40e / Ribosomal protein L27e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L44e / Ribosomal Protein L6, KOW domain / Ribosomal protein L44 / Ribosomal protein 60S L18 and 50S L18e / 60S ribosomal protein L35 / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L6e / : / Ribosomal protein L7A/L8 / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L6E / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L30/YlxQ / 60S ribosomal protein L19 / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L31e, conserved site / : / Ribosomal protein L31e signature. / Ribosomal protein L36e / Ribosomal protein L14e domain / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L14 / Ribosomal protein L18e / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / : / : / Ribosomal protein L19e, C-terminal domain
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60s ribosomal protein l27a-3 / 60S ribosomal protein L35-like / 60S ribosomal protein L30 / 60S ribosomal protein L11-1 / 60S ribosomal protein L27 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60s ribosomal protein l27a-3 / 60S ribosomal protein L35-like / 60S ribosomal protein L30 / 60S ribosomal protein L11-1 / 60S ribosomal protein L27 / 60S ribosomal protein L21-1-like / 60S ribosomal protein L5-like / Ribosomal protein L15 / 60S ribosomal protein L23 / 60S ribosomal protein L8-like / Ribosomal protein / 60S ribosomal protein L31 / 60S ribosomal protein L10 / Large ribosomal subunit protein uL13w / 60S ribosomal protein L3 / Ribosomal protein L19 / Large ribosomal subunit protein eL33y-like / 60S ribosomal protein L24 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4-like / 60S ribosomal protein L38 / Large ribosomal subunit protein uL24z / Large ribosomal subunit protein uL6z/uL6y / 60S ribosomal protein L13 / 60S ribosomal protein L18-2 / Ribosomal protein L37 / Large ribosomal subunit protein uL22z / Large ribosomal subunit protein eL14z / 60S ribosomal protein L18a / 60S ribosomal protein L36 / Large ribosomal subunit protein eL6-like / Large ribosomal subunit protein eL28z-like / Large ribosomal subunit protein uL30w-like / Ubiquitin-ribosomal protein eL40 fusion protein / 60S ribosomal protein L7a / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL39x / Large ribosomal subunit protein eL32z / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL23
Similarity search - Component
Biological speciesNicotiana benthamiana (plant)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLu, G. / Lin, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130063 China
National Natural Science Foundation of China (NSFC)32471349 China
CitationJournal: To be published
Title: cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 60S
Authors: Lu, G. / Lin, J.
History
DepositionJul 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
LA: Ribosomal protein
LB: 60S ribosomal protein L8-like
LC: 60S ribosomal protein L3
LD: 60S ribosomal protein L4-like
LE: 60S ribosomal protein L11-1
LF: 60S ribosomal protein L9-1
LG: 60S ribosomal protein L13a-4
LH: 60S ribosomal protein L23
LI: 60s ribosomal protein l27a-3
LJ: 60S ribosomal protein L10
LK: 60S ribosomal protein L5-like
LL: 60S ribosomal protein L17-1 isoform X2
LM: Large ribosomal subunit protein uL23
LN: 60S ribosomal protein L26-1
LO: 60S ribosomal protein L35-like
LP: 60S ribosomal protein L7-4-like
LQ: 60S ribosomal protein L6-like isoform X1
LR: 60S ribosomal protein L7a
LS: 60S ribosomal protein L13
LT: 60S ribosomal protein L14-1
LU: Ribosomal protein L15
LV: 60S ribosomal protein L18-2
LW: Ribosomal protein L19
LX: 60S ribosomal protein L18a
LY: 60S ribosomal protein L21-1-like
LZ: Large ribosomal subunit protein eL22
La: 60S ribosomal protein L24
Lb: 60S ribosomal protein L27
Lc: 60S ribosomal protein L28-1-like
Ld: 60S ribosomal protein L29
Le: 60S ribosomal protein L30
Lf: 60S ribosomal protein L31
Lg: 60S ribosomal protein L32-1
Lh: 60S ribosomal protein L35a-3-like
Li: Large ribosomal subunit protein eL34
Lj: 60S ribosomal protein L36
Lk: Ribosomal protein L37
Ll: 60S ribosomal protein L38
Lm: 60S ribosomal protein L39-3
Ln: Ubiquitin-60S ribosomal protein L40
Lp: 60S ribosomal protein L44
Lq: 60S ribosomal protein L37a
10: RNA (204-MER)
12: 5S rRNA
13: 5.8S rRNA
14: 25S rRNA


Theoretical massNumber of molelcules
Total (without water)2,060,31546
Polymers2,060,31546
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules LALn

#1: Protein Ribosomal protein


Mass: 24778.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3Y379
#40: Protein Ubiquitin-60S ribosomal protein L40


Mass: 14703.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7X7W2

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60S ribosomal protein ... , 34 types, 34 molecules LBLCLDLELFLGLHLILJLKLLLNLOLPLQLRLSLTLVLXLYLaLbLcLdLeLfLgLhLj...

#2: Protein 60S ribosomal protein L8-like


Mass: 28220.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XXQ5
#3: Protein 60S ribosomal protein L3


Mass: 44552.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3ZLI9
#4: Protein 60S ribosomal protein L4-like


Mass: 44778.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4BWA4
#5: Protein 60S ribosomal protein L11-1


Mass: 20794.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XAW1
#6: Protein 60S ribosomal protein L9-1


Mass: 22058.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4CJ62
#7: Protein 60S ribosomal protein L13a-4


Mass: 23583.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3Z662
#8: Protein 60S ribosomal protein L23 / Large ribosomal subunit protein uL14


Mass: 15040.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XSQ1
#9: Protein 60s ribosomal protein l27a-3


Mass: 16504.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1J6IJF4
#10: Protein 60S ribosomal protein L10


Mass: 24841.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3Z2D7
#11: Protein 60S ribosomal protein L5-like


Mass: 33691.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XE16
#12: Protein 60S ribosomal protein L17-1 isoform X2


Mass: 19906.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4DQP0
#14: Protein 60S ribosomal protein L26-1


Mass: 16808.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4CC07
#15: Protein 60S ribosomal protein L35-like


Mass: 14324.413 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3WY31
#16: Protein 60S ribosomal protein L7-4-like


Mass: 28147.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7X2X8
#17: Protein 60S ribosomal protein L6-like isoform X1


Mass: 25493.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7WD54
#18: Protein 60S ribosomal protein L7a


Mass: 27223.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7XNI3
#19: Protein 60S ribosomal protein L13


Mass: 22862.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4CSN1
#20: Protein 60S ribosomal protein L14-1


Mass: 15027.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7UYX7
#22: Protein 60S ribosomal protein L18-2


Mass: 20905.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4DF55
#24: Protein 60S ribosomal protein L18a


Mass: 21513.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7V5H1
#25: Protein 60S ribosomal protein L21-1-like


Mass: 18716.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XCW6
#27: Protein 60S ribosomal protein L24


Mass: 18606.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4BHF2
#28: Protein 60S ribosomal protein L27


Mass: 15692.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XBV7
#29: Protein 60S ribosomal protein L28-1-like


Mass: 15987.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7WYY1
#30: Protein/peptide 60S ribosomal protein L29


Mass: 5914.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant)
#31: Protein 60S ribosomal protein L30


Mass: 12420.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3WZ09
#32: Protein 60S ribosomal protein L31


Mass: 13894.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3Y3V5
#33: Protein 60S ribosomal protein L32-1


Mass: 15637.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7YAK1
#34: Protein 60S ribosomal protein L35a-3-like


Mass: 12959.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4AHL7
#36: Protein 60S ribosomal protein L36


Mass: 12389.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7VXX3
#38: Protein 60S ribosomal protein L38


Mass: 8101.704 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4C4G8
#39: Protein 60S ribosomal protein L39-3


Mass: 6503.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7Y1K3
#41: Protein 60S ribosomal protein L44


Mass: 11991.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7YPT7
#42: Protein 60S ribosomal protein L37a


Mass: 8624.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7XSD1

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Large ribosomal subunit protein ... , 3 types, 3 molecules LMLZLi

#13: Protein Large ribosomal subunit protein uL23 / 60S ribosomal protein L23a / L25


Mass: 17355.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: Q07761
#26: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 12506.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4BSU3
#35: Protein Large ribosomal subunit protein eL34 / 60S ribosomal protein L34


Mass: 13788.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: P41098

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Ribosomal protein ... , 3 types, 3 molecules LULWLk

#21: Protein Ribosomal protein L15


Mass: 24226.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XIA7
#23: Protein Ribosomal protein L19


Mass: 24742.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4A7M5
#37: Protein Ribosomal protein L37


Mass: 10879.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4DN51

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RNA chain , 4 types, 4 molecules 10121314

#43: RNA chain RNA (204-MER)


Mass: 65633.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#44: RNA chain 5S rRNA


Mass: 38328.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: GenBank: 2501293102
#45: RNA chain 5.8S rRNA


Mass: 52534.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant)
#46: RNA chain 25S rRNA


Mass: 1097118.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant)

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Details

Has protein modificationN

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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: tobacco 80S ribosome with tRNA-like structure / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Nicotiana benthamiana (plant)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k)

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Processing

EM software
IDNameCategory
1EPUparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53930 / Symmetry type: POINT

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