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Basic information

Entry
Database: PDB / ID: 8jiv
TitleAtomic structure of wheat ribosome reveals unique features of the plant ribosomes
Components
  • (60S ribosomal protein ...) x 19
  • (Genome assembly, chromosome: ...) x 3
  • (Ribosomal protein ...) x 15
  • 25S rRNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • KOW domain-containing protein
  • Ribosomal L28e/Mak16 domain-containing protein
  • TRASH domain-containing protein
  • Ubiquitin-like domain-containing protein
KeywordsRIBOSOME / Protein Synthesis Machinery / Eukaryotic Ribosome / Plant / TRANSLATION
Function / homology
Function and homology information


protein-RNA complex assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / ribosome biogenesis / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit ...protein-RNA complex assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / ribosome biogenesis / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal protein L28e / Ribosomal protein L2, archaeal-type / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L10e, conserved site ...Ribosomal protein L28e / Ribosomal protein L2, archaeal-type / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L27e, conserved site / : / Ribosomal protein L24e, conserved site / Ribosomal protein L34e, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L38e protein family / Ribosomal L22e protein family / Ribosomal protein L23/L25, N-terminal / 60S ribosomal protein L35 / Ribosomal protein L30e, conserved site / Ribosomal protein L44 / Ribosomal protein L34Ae / Ribosomal protein L23, N-terminal domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / Ribosomal protein L30/YlxQ / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L34e / Ribosomal protein L37ae / Ribosomal protein L14e domain / 60S ribosomal protein L6E / Ribosomal protein L19, eukaryotic / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal L40e family / Ribosomal protein L36e / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L7A/L8 / Ribosomal protein L27e signature. / Ribosomal protein L10e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L7, eukaryotic / Ribosomal protein L6e / Ribosomal protein L14 / Ribosomal protein L30, N-terminal / Ribosomal protein L6, conserved site-2 / Ribosomal protein L14, KOW motif / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e conserved site / Ribosomal protein L14 / Ribosomal L37ae protein family / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L39e, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L19e signature. / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L24e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L6e signature. / Ribosomal_L31e / Ribosomal protein L15e, conserved site / Ribosomal protein L30e signature 1. / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / 60S ribosomal protein L19 / Ribosomal protein L37e, conserved site / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L36e signature. / Ribosomal protein L37e / Ribosomal protein L39e signature. / Ribosomal protein L21e / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal protein L32e / Ribosomal protein L32e superfamily / Ribosomal_L32e / Ribosomal protein L31e
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL6 alpha-beta domain-containing protein / 60S ribosomal protein L29 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL6 alpha-beta domain-containing protein / 60S ribosomal protein L29 / 60S ribosomal protein L36 / Large ribosomal subunit protein uL23 N-terminal domain-containing protein / 60S ribosomal protein L38 / Ubiquitin-like domain-containing protein / Ribosomal protein L37 / 60S ribosomal protein L27 / 60S ribosomal protein L11 / 60S ribosomal protein L18a / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Ribosomal protein L19 / Large ribosomal subunit protein uL18 C-terminal eukaryotes domain-containing protein / Large ribosomal subunit protein eL14 domain-containing protein / Uncharacterized protein / TRASH domain-containing protein / KOW domain-containing protein / Uncharacterized protein / 60S ribosomal protein L13 / 60S ribosomal protein L6 / 60S ribosomal protein L7a / 60S ribosomal protein L34 / 60S ribosomal protein L32 / 60S ribosomal protein L37a, expressed / 60S ribosomal protein L21 / Ribosomal protein L17 / Ribosomal protein L39 / Ribosomal protein L13a / Ribosomal protein L3 / Large ribosomal subunit protein uL29 / Ribosomal protein eL8/eL30/eS12/Gadd45 domain-containing protein / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL2 C-terminal domain-containing protein / Ribosomal protein L15 / Uncharacterized protein / 60S ribosomal protein L31 / Uncharacterized protein
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsMishra, R.K. / Sharma, P. / Hussain, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Citation
Journal: Structure / Year: 2024
Title: Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes.
Authors: Rishi Kumar Mishra / Prafful Sharma / Faisal Tarique Khaja / Adwaith B Uday / Tanweer Hussain /
Abstract: Plants being sessile organisms exhibit unique features in ribosomes, which might aid in rapid gene expression and regulation in response to varying environmental conditions. Here, we present high- ...Plants being sessile organisms exhibit unique features in ribosomes, which might aid in rapid gene expression and regulation in response to varying environmental conditions. Here, we present high-resolution structures of the 60S and 80S ribosomes from wheat, a monocot staple crop plant (Triticum aestivum). While plant ribosomes have unique plant-specific rRNA modification (Cm1847) in the peptide exit tunnel (PET), the zinc-finger motif in eL34 is absent, and uL4 is extended, making an exclusive interaction network. We note differences in the eL15-helix 11 (25S) interaction, eL6-ES7 assembly, and certain rRNA chemical modifications between monocot and dicot ribosomes. In eukaryotes, we observe highly conserved rRNA modification (Gm75) in 5.8S rRNA and a flipped base (G1506) in PET. These features are likely involved in sensing or stabilizing nascent chain. Finally, we discuss the importance of the universal conservation of three consecutive rRNA modifications in all ribosomes for their interaction with A-site aminoacyl-tRNA.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Uday, A.B. / Khaja, F.T.
History
DepositionMay 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Aa: 25S rRNA
Ab: 5S rRNA
Ac: 5.8S rRNA
CA: Ribosomal protein L2 C-terminal domain-containing protein
CB: Ribosomal protein L3
CC: 60S ribosomal protein L4 C-terminal domain-containing protein
CD: Ribosomal protein L5 eukaryotic C-terminal domain-containing protein
CE: 60S ribosomal protein L6
CF: 60S ribosomal protein uL30
CG: 60S ribosomal protein L7a
CH: Ribosomal protein L6 alpha-beta domain-containing protein
CI: Ribosomal protein L10e/L16 domain-containing protein
CJ: 60S ribosomal protein L11
CL: 60S ribosomal protein L13
CM: Ribosomal protein L14e domain-containing protein
CN: Ribosomal protein L15
CO: Ribosomal protein L13a
CP: 60S ribosomal protein uL22
CQ: Ribosomal protein L18e/L15P domain-containing protein
CR: Ribosomal protein L19
CS: 60S ribosomal protein L18a
CT: 60S ribosomal protein L21
CU: Genome assembly, chromosome: II
CV: Ribosomal protein L17
CW: TRASH domain-containing protein
CX: Genome assembly, chromosome: II
CY: KOW domain-containing protein
CZ: 60S ribosomal protein L27
Ca: Ribosomal protein L18e/L15P domain-containing protein
Cb: 60S ribosomal protein L29
Cc: Ribosomal protein L7Ae/L30e/S12e/Gadd45 domain-containing protein
Cd: 60S ribosomal protein L31
Ce: 60S ribosomal protein eL32
Cf: 60S ribosomal protein eL33
Cg: 60S ribosomal protein L34
Ch: 60S ribosomal protein L35
Ci: 60S ribosomal protein L36
Cj: Ribosomal protein L37
Ck: 60S ribosomal protein L38
Cl: Ribosomal protein L39
Cm: Ubiquitin-like domain-containing protein
Co: Genome assembly, chromosome: II
Cp: 60S ribosomal protein L37a, expressed
Cr: Ribosomal L28e/Mak16 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,984,466361
Polymers1,975,57344
Non-polymers8,893317
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules AaAbAc

#1: RNA chain 25S rRNA


Mass: 1098269.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: GenBank: 2123606587
#2: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38411.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: GenBank: X06094.1
#3: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50953.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: GenBank: AF438188.1

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Ribosomal protein ... , 15 types, 15 molecules CACBCDCHCICMCNCOCQCRCVCaCcCjCl

#4: Protein Ribosomal protein L2 C-terminal domain-containing protein / Ribosome


Mass: 28251.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5ECL2
#5: Protein Ribosomal protein L3 / / Ribosomal protein L3-A1 / Ribosomal protein L3A-1


Mass: 44262.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q7X744
#7: Protein Ribosomal protein L5 eukaryotic C-terminal domain-containing protein / Ribosome


Mass: 35341.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6DD91
#11: Protein Ribosomal protein L6 alpha-beta domain-containing protein / Ribosome


Mass: 21301.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A077RTE5
#12: Protein Ribosomal protein L10e/L16 domain-containing protein / Ribosome


Mass: 24516.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6HUM3
#15: Protein Ribosomal protein L14e domain-containing protein / Ribosome


Mass: 15490.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6DGT8
#16: Protein Ribosomal protein L15 /


Mass: 24488.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FEX7
#17: Protein Ribosomal protein L13a / Ribosome


Mass: 23581.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L1
#19: Protein Ribosomal protein L18e/L15P domain-containing protein / Ribosome


Mass: 21351.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B5ZQE8
#20: Protein Ribosomal protein L19 /


Mass: 24059.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6C2W3
#24: Protein Ribosomal protein L17 /


Mass: 14536.206 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K4
#29: Protein Ribosomal protein L18e/L15P domain-containing protein / Ribosome


Mass: 16068.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6AUW8
#31: Protein Ribosomal protein L7Ae/L30e/S12e/Gadd45 domain-containing protein / Ribosome


Mass: 12372.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W4ZRU3
#38: Protein Ribosomal protein L37 /


Mass: 10765.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D6BC85
#40: Protein Ribosomal protein L39 /


Mass: 6528.786 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K7

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60S ribosomal protein ... , 19 types, 19 molecules CCCECFCGCJCLCPCSCTCZCbCdCeCfCgChCiCkCp

#6: Protein 60S ribosomal protein L4 C-terminal domain-containing protein / Ribosome


Mass: 44822.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#8: Protein 60S ribosomal protein L6 /


Mass: 25924.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6QGW3
#9: Protein 60S ribosomal protein uL30 /


Mass: 28161.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6DM38
#10: Protein 60S ribosomal protein L7a /


Mass: 29407.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6RED0
#13: Protein 60S ribosomal protein L11 /


Mass: 20725.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B5XX39
#14: Protein 60S ribosomal protein L13 /


Mass: 24170.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6QBU0
#18: Protein 60S ribosomal protein uL22 /


Mass: 19525.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FSM8
#21: Protein 60S ribosomal protein L18a /


Mass: 21296.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B5Z5M6
#22: Protein 60S ribosomal protein L21 /


Mass: 18719.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: F4YWL9
#28: Protein 60S ribosomal protein L27 /


Mass: 15615.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A341XZK6
#30: Protein 60S ribosomal protein L29 /


Mass: 6994.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D5RRD3
#32: Protein 60S ribosomal protein L31 /


Mass: 14152.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5G990
#33: Protein 60S ribosomal protein eL32 /


Mass: 15737.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6SDD9
#34: Protein 60S ribosomal protein eL33 /


Mass: 12684.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#35: Protein 60S ribosomal protein L34 /


Mass: 13798.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6RFY8
#36: Protein 60S ribosomal protein L35 /


Mass: 14401.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L805
#37: Protein 60S ribosomal protein L36 /


Mass: 12594.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D5S805
#39: Protein 60S ribosomal protein L38 /


Mass: 8115.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D5W6Q2
#43: Protein 60S ribosomal protein L37a, expressed / Ribosome


Mass: 10266.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: D8L9P6

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Genome assembly, chromosome: ... , 3 types, 3 molecules CUCXCo

#23: Protein Genome assembly, chromosome: II


Mass: 14372.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5C5N9
#26: Protein Genome assembly, chromosome: II


Mass: 16920.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D5UQZ5
#42: Protein Genome assembly, chromosome: II


Mass: 12152.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5HX73

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Protein , 4 types, 4 molecules CWCYCmCr

#25: Protein TRASH domain-containing protein


Mass: 18293.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6ELC9
#27: Protein KOW domain-containing protein


Mass: 14735.380 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6GQI2
#41: Protein Ubiquitin-like domain-containing protein


Mass: 14828.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D5XNC2
#44: Protein Ribosomal L28e/Mak16 domain-containing protein


Mass: 16607.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B5ZZN9

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Non-polymers , 3 types, 317 molecules

#45: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#46: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 242 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#47: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: The large subunit of wheat Ribosome / Type: RIBOSOME / Entity ID: #1-#44 / Source: NATURAL
Source (natural)Organism: Triticum aestivum (bread wheat)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample is the large subunit of wheat ribosome
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 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: OTHER
Electron lensMode: OTHER / Calibrated magnification: 75000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / C2 aperture diameter: 2.7 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 44.6 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105563 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 19.63 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0053125269
ELECTRON MICROSCOPYf_angle_d0.6912184300
ELECTRON MICROSCOPYf_chiral_restr0.041522858
ELECTRON MICROSCOPYf_plane_restr0.005611657
ELECTRON MICROSCOPYf_dihedral_angle_d14.811143514

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