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Basic information

Entry
Database: PDB / ID: 9phc
TitleIn vitro reconstituted complex of purified S. pombe large ribosomal subunit and SNOR
Components
  • (Large ribosomal subunit protein ...) x 40
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • SDO1-like protein C21C3.19
KeywordsRIBOSOME / 60S / large subunit / SNOR / pombe / Yeast / Hibernating / Glucose
Function / homology
Function and homology information


L13a-mediated translational silencing of Ceruloplasmin expression / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / ribonuclease MRP complex / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome / tRNA processing / cytosolic large ribosomal subunit assembly ...L13a-mediated translational silencing of Ceruloplasmin expression / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / ribonuclease MRP complex / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome / tRNA processing / cytosolic large ribosomal subunit assembly / pre-mRNA intronic binding / protein-RNA complex assembly / maturation of LSU-rRNA / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA processing / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / negative regulation of gene expression / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Ribosome maturation protein Sdo1/SBDS-like / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily / Shwachman-Bodian-Diamond syndrome (SBDS) N-terminal domain / : / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. ...Ribosome maturation protein Sdo1/SBDS-like / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily / Shwachman-Bodian-Diamond syndrome (SBDS) N-terminal domain / : / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L6e signature. / Ribosomal protein L44e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 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 L36e signature. / Ribosomal protein L30e signature 1. / Ribosomal protein L44e / Ribosomal protein L44 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L35Ae, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / : / Ribosomal Protein L6, KOW domain / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L35 / Ribosomal protein L30e signature 2. / Ribosomal protein L7A/L8 / Ribosomal protein L30e, conserved site / : / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein L6e / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / 60S ribosomal protein L6E / : / Ribosomal protein L30/YlxQ / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L18e / Ribosomal protein L14e domain / Ribosomal protein L31e, conserved site / Ribosomal protein L14 / Ribosomal protein L31e signature. / : / : / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L37ae / Ribosomal L37ae protein family
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein uL22A ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL19B / Large ribosomal subunit protein eL21B / Large ribosomal subunit protein uL13A / Large ribosomal subunit protein uL30C / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL18B / Large ribosomal subunit protein eL24B / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL6B / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL36B / Large ribosomal subunit protein eL37B / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL14B / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein uL2C / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein uL3A / Large ribosomal subunit protein eL30A / Large ribosomal subunit protein uL15B / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL32A / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL16A / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL23A / Large ribosomal subunit protein eL18B / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL43A / SDO1-like protein C21C3.19 / Large ribosomal subunit protein eL34B / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL15B / Large ribosomal subunit protein eL38A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL42
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsGluc, M. / Jomaa, A.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: Nature / Year: 2026
Title: SNOR promotes translation restart after dormancy.
Authors: Maciej Gluc / Higor Rosa / Maria Bozko / Lesley A Turner / Cassidy R Prince / Yelena Peskova / Heather A Feaga / Kathleen L Gould / Simone Mattei / Ahmad Jomaa /
Abstract: Cellular dormancy enables survival during prolonged nutrient limitation by reversibly suppressing protein synthesis. How inactive eukaryotic ribosomes are reactivated when nutrients return remains ...Cellular dormancy enables survival during prolonged nutrient limitation by reversibly suppressing protein synthesis. How inactive eukaryotic ribosomes are reactivated when nutrients return remains unclear. Here, using high-resolution in situ cryo-electron tomography in Schizosaccharomyces pombe, we identify SNOR, an SBDS domain-containing ribosome-associated factor that binds at the peptidyl transferase centre and contacts the hypusinated loop of eIF5A during glucose depletion-induced dormancy. Rather than acting as a canonical hibernation factor, SNOR licenses dormant ribosomes for rapid translational restart. Upon glucose repletion, SNOR and eIF5A act together to promote efficient recovery of polysomes and exit from dormancy. These findings define a stress-responsive ribosome restart module that couples carbon-source limitation to surveillance of the ribosomal active site and reactivation of protein synthesis.
History
DepositionJul 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B0: Large ribosomal subunit protein eL42
B1: Large ribosomal subunit protein eL43A
B2: 28S ribosomal RNA
B3: 5S ribosomal RNA
B4: 5.8S ribosomal RNA
BN: Large ribosomal subunit protein uL2C
BO: Large ribosomal subunit protein uL3A
BP: Large ribosomal subunit protein uL4A
BQ: Large ribosomal subunit protein uL18B
BR: Large ribosomal subunit protein eL6
BS: Large ribosomal subunit protein uL30C
BT: Large ribosomal subunit protein eL8
BU: Large ribosomal subunit protein uL6B
BV: Large ribosomal subunit protein uL16A
BW: Large ribosomal subunit protein uL5A
BX: Large ribosomal subunit protein eL13
BY: Large ribosomal subunit protein eL14
BZ: Large ribosomal subunit protein eL15B
Ba: Large ribosomal subunit protein uL13A
Bb: Large ribosomal subunit protein uL22A
Bc: Large ribosomal subunit protein eL18B
Bd: Large ribosomal subunit protein eL19B
Be: Large ribosomal subunit protein eL20A
Bf: Large ribosomal subunit protein eL21B
Bg: Large ribosomal subunit protein eL22
Bh: Large ribosomal subunit protein uL14B
Bi: Large ribosomal subunit protein eL24B
Bj: Large ribosomal subunit protein uL23A
Bk: Large ribosomal subunit protein uL24
Bl: Large ribosomal subunit protein eL27A
Bm: Large ribosomal subunit protein uL15B
Bn: Large ribosomal subunit protein eL29
Bo: Large ribosomal subunit protein eL30A
Bp: Large ribosomal subunit protein eL31
Bq: Large ribosomal subunit protein eL32A
Br: Large ribosomal subunit protein eL33A
Bs: Large ribosomal subunit protein eL34B
Bt: Large ribosomal subunit protein uL29
Bu: Large ribosomal subunit protein eL36B
Bv: Large ribosomal subunit protein eL37B
Bw: Large ribosomal subunit protein eL38A
Bx: Large ribosomal subunit protein eL39
By: Large ribosomal subunit protein eL28
HS: SDO1-like protein C21C3.19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,019,21847
Polymers2,019,02244
Non-polymers1963
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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Large ribosomal subunit protein ... , 40 types, 40 molecules B0B1BNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBdBeBfBgBhBiBjBkBlBmBnBo...

#1: Protein Large ribosomal subunit protein eL42 / 60S ribosomal protein L42


Mass: 12239.647 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: Q9UTI8
#2: Protein Large ribosomal subunit protein eL43A / 60S ribosomal protein L43-A / L37A


Mass: 10444.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: Q9HGL8
#6: Protein Large ribosomal subunit protein uL2C / 60S ribosomal protein L2-C / K37 / K5 / KD4


Mass: 27151.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: P0CT72
#7: Protein Large ribosomal subunit protein uL3A / 60S ribosomal protein L3-A / SP-L1


Mass: 43889.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: P40372
#8: Protein Large ribosomal subunit protein uL4A / 60S ribosomal protein L4-A / L2


Mass: 39839.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: P35679
#9: Protein Large ribosomal subunit protein uL18B / 60S ribosomal protein L5-B


Mass: 33538.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O74306
#10: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6


Mass: 21285.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: P79071
#11: Protein Large ribosomal subunit protein uL30C / 60S ribosomal protein L7-C


Mass: 28780.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O60143
#12: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L8 / L4 / L7A


Mass: 28659.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O13672
#13: Protein Large ribosomal subunit protein uL6B / 60S ribosomal protein L9-B


Mass: 21413.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O74905
#14: Protein Large ribosomal subunit protein uL16A / 60S ribosomal protein L10-A / QM protein homolog / SpQM


Mass: 25421.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: Q09127
#15: Protein Large ribosomal subunit protein uL5A / 60S ribosomal protein L11-A


Mass: 19928.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: P0CT77
#16: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13


Mass: 23578.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O74175
#17: Protein Large ribosomal subunit protein eL14 / 60S ribosomal protein L14


Mass: 15241.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O94238
#18: Protein Large ribosomal subunit protein eL15B / 60S ribosomal protein L15-B / SP-L12


Mass: 23878.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: Q9US22
#19: Protein Large ribosomal subunit protein uL13A / 60S ribosomal protein L16-A


Mass: 22050.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O42848
#20: Protein Large ribosomal subunit protein uL22A / 60S ribosomal protein L17-A


Mass: 20854.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O14339
#21: Protein Large ribosomal subunit protein eL18B / 60S ribosomal protein L18-B


Mass: 21234.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: Q8TFH1
#22: Protein Large ribosomal subunit protein eL19B / 60S ribosomal protein L19-B


Mass: 22813.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O42699
#23: Protein Large ribosomal subunit protein eL20A / 60S ribosomal protein L20-A / SP-L17


Mass: 20642.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: P0CT68
#24: Protein Large ribosomal subunit protein eL21B / 60S ribosomal protein L21-B


Mass: 18390.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O42706
#25: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 13344.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: Q09668
#26: Protein Large ribosomal subunit protein uL14B / 60S ribosomal protein L23-B


Mass: 14905.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: P0CT61
#27: Protein Large ribosomal subunit protein eL24B / 60S ribosomal protein L24-B


Mass: 16957.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O74884
#28: Protein Large ribosomal subunit protein uL23A / 60S ribosomal protein L25-A


Mass: 15870.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: Q10330
#29: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26


Mass: 14375.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: P78946
#30: Protein Large ribosomal subunit protein eL27A / 60S ribosomal protein L27-A


Mass: 15421.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O14388
#31: Protein Large ribosomal subunit protein uL15B / 60S ribosomal protein L28-B


Mass: 16723.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: P57728
#32: Protein Large ribosomal subunit protein eL29 / 60S ribosomal protein L29 / L43


Mass: 7224.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: Q92366
#33: Protein Large ribosomal subunit protein eL30A / 60S ribosomal protein L30-1 / L32


Mass: 11610.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: P52808
#34: Protein Large ribosomal subunit protein eL31 / 60S ribosomal protein L31


Mass: 13290.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: Q9URX6
#35: Protein Large ribosomal subunit protein eL32A / 60S ribosomal protein L32-A


Mass: 14491.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: P79015
#36: Protein Large ribosomal subunit protein eL33A / 60S ribosomal protein L33-A / L37A


Mass: 12212.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: Q9USX4
#37: Protein Large ribosomal subunit protein eL34B / 60S ribosomal protein L34-2 / 60S ribosomal protein L34-B


Mass: 12828.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: Q9URT8
#38: Protein Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


Mass: 14333.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O74904
#39: Protein Large ribosomal subunit protein eL36B / 60S ribosomal protein L36-B


Mass: 11287.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O94658
#40: Protein Large ribosomal subunit protein eL37B / 60S ribosomal protein L37-B / SP-L27


Mass: 10112.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: P05733
#41: Protein Large ribosomal subunit protein eL38A / 60S ribosomal protein L38-1


Mass: 8511.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: Q9USR7
#42: Protein Large ribosomal subunit protein eL39 / 60S ribosomal protein L39 / SP-L36


Mass: 6326.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: P05767
#43: Protein Large ribosomal subunit protein eL28 / Probable 60S ribosomal protein L28e


Mass: 14781.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O14069

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RNA chain , 3 types, 3 molecules B2B3B4

#3: RNA chain 28S ribosomal RNA


Mass: 1129828.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: GenBank: 157310483
#4: RNA chain 5S ribosomal RNA


Mass: 78518.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: GenBank: 157310380
#5: RNA chain 5.8S ribosomal RNA


Mass: 52880.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / References: GenBank: 288694

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Protein / Non-polymers , 2 types, 4 molecules HS

#44: Protein SDO1-like protein C21C3.19


Mass: 11909.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Gene: SPBC21C3.19
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9P7K6
#45: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
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: In vitro reconstituted complex of purified S. pombe large ribosomal subunit and SNOR
Type: RIBOSOME / Entity ID: #1-#44 / Source: MULTIPLE SOURCES
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.4
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2PHENIX1.21.2_5419model refinement
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110548 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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