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- PDB-6fai: Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit -

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Entry
Database: PDB / ID: 6fai
TitleStructure of a eukaryotic cytoplasmic pre-40S ribosomal subunit
Components
  • (40S ribosomal protein ...) x 29
  • 20S ribosomal RNA
  • Essential nuclear protein 1
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Pre-rRNA-processing protein PNO1
  • Protein LTV1
  • Ribosome biogenesis protein TSR1
  • Serine/threonine-protein kinase RIO2
KeywordsRIBOSOME / pre-40S ribosme / cryo-EM / ribosome assembly / ribosomes / ribosome biogenesis
Function / homology
Function and homology information


positive regulation of RNA import into nucleus / Ragulator complex => GO:0071986 / ATP export / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / regulation of cellular response to stress / invasive growth in response to glucose limitation / U3 snoRNA binding ...positive regulation of RNA import into nucleus / Ragulator complex => GO:0071986 / ATP export / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / regulation of cellular response to stress / invasive growth in response to glucose limitation / U3 snoRNA binding / GDP-dissociation inhibitor activity / poly(A)+ mRNA export from nucleus / rRNA export from nucleus / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / preribosome, small subunit precursor / mRNA destabilization / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / rescue of stalled ribosome / snoRNA binding / G-protein alpha-subunit binding / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / ribosomal small subunit export from nucleus / ribonucleoprotein complex binding / maturation of SSU-rRNA / regulation of translational fidelity / response to osmotic stress / small-subunit processome / ribosomal small subunit biogenesis / late endosome membrane / protein kinase A catalytic subunit binding / proteasome assembly / maintenance of translational fidelity / positive regulation of translational fidelity / translational termination / protein kinase C binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / rRNA processing / cytoplasmic stress granule / cytoplasmic translation / ribosome binding / ribosome biogenesis / unfolded protein binding / cytosolic small ribosomal subunit / small ribosomal subunit / cellular response to oxidative stress / protein localization / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / non-specific serine/threonine protein kinase / translation / GTPase activity / protein kinase activity / negative regulation of gene expression / positive regulation of protein phosphorylation / mRNA binding / G protein-coupled receptor signaling pathway / GTP binding / protein threonine kinase activity / protein serine kinase activity / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Ribosomal protein S17, conserved site / WD40 repeat, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3, conserved site ...Ribosomal protein S17, conserved site / WD40 repeat, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S2, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Ribosomal protein S15P / Ribosomal protein S19/S15, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S5, N-terminal, conserved site / Ribosomal S11, conserved site / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S12/S23 / Ribosomal protein S30 / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Low temperature viability protein Ltv1 / Bystin / K homology domain superfamily, prokaryotic type / Ribosomal protein S17 / Ribosomal protein S13-like, H2TH / Protein kinase-like domain superfamily / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal protein L23/L15e core domain superfamily / Ribosomal S24e conserved site / AARP2CN / Ribosomal protein S5, N-terminal / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / RIO2 kinase winged helix domain, N-terminal / WD40/YVTN repeat-like-containing domain superfamily / K homology domain-like, alpha/beta / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal protein S2, eukaryotic / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S11 / Ribosomal protein S28e / Ribosomal protein S27 / S25 ribosomal protein / Ribosomal protein S24e / Ribosomal protein S12/S23 / Ribosomal protein S8 / Ribosomal protein S21e / Ribosomal protein S10p/S20e / Ribosomal protein S13/S18 / Ribosomal S17 / Ribosomal protein S9/S16 / Ribosomal protein S15 / WD domain, G-beta repeat / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal_S17 N-terminal / Ribosomal S3Ae family / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S3, C-terminal domain / KH domain / KOW motif / Ribosomal family S4e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S7e / Ribosomal protein S8e / Ribosomal protein S30 / Krr1 KH1 domain / Ribosomal protein S28e conserved site / Ribosomal protein S7 domain superfamily / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / Serine/threonine-protein kinase Rio2 / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S3, C-terminal domain superfamily
gb:874346701: / Pre-rRNA-processing protein PNO1 / 40S ribosomal protein S20 / 40S ribosomal protein S0-A / 40S ribosomal protein S1-A / Protein LTV1 / 40S ribosomal protein S27-A / Guanine nucleotide-binding protein subunit beta-like protein / Essential nuclear protein 1 / Serine/threonine-protein kinase RIO2 ...gb:874346701: / Pre-rRNA-processing protein PNO1 / 40S ribosomal protein S20 / 40S ribosomal protein S0-A / 40S ribosomal protein S1-A / Protein LTV1 / 40S ribosomal protein S27-A / Guanine nucleotide-binding protein subunit beta-like protein / Essential nuclear protein 1 / Serine/threonine-protein kinase RIO2 / 40S ribosomal protein S5 / 40S ribosomal protein S29-A / 40S ribosomal protein S12 / 40S ribosomal protein S15 / Ribosome biogenesis protein TSR1 / 40S ribosomal protein S25-A / 40S ribosomal protein S28-A / 40S ribosomal protein S7-A / 40S ribosomal protein S2 / 40S ribosomal protein S17-A / 40S ribosomal protein S23-A / 40S ribosomal protein S3 / 40S ribosomal protein S13 / 40S ribosomal protein S14-A / 40S ribosomal protein S19-A / 40S ribosomal protein S21-A / 40S ribosomal protein S22-A / 40S ribosomal protein S24-A / 40S ribosomal protein S18-A / 40S ribosomal protein S30-A / 40S ribosomal protein S4-A / 40S ribosomal protein S6-A / 40S ribosomal protein S8-A / 40S ribosomal protein S11-A / 40S ribosomal protein S16-A / 40S ribosomal protein S9-A
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsScaiola, A. / Pena, C. / Weisser, M. / Boehringer, D. / Leibundgut, M. / Klingauf-Nerurkar, P. / Gerhardy, S. / Panse, V.G. / Ban, N.
CitationJournal: EMBO J / Year: 2018
Title: Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit.
Authors: Alain Scaiola / Cohue Peña / Melanie Weisser / Daniel Böhringer / Marc Leibundgut / Purnima Klingauf-Nerurkar / Stefan Gerhardy / Vikram Govind Panse / Nenad Ban /
Abstract: Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron ...Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron microscopy (cryo-EM), we have determined the structure of a yeast cytoplasmic pre-40S particle in complex with Enp1, Ltv1, Rio2, Tsr1, and Pno1 assembly factors poised to initiate final maturation. The structure reveals that the pre-rRNA adopts a highly distorted conformation of its 3' major and 3' minor domains stabilized by the binding of the assembly factors. This observation is consistent with a mechanism that involves concerted release of the assembly factors orchestrated by the folding of the rRNA in the head of the pre-40S subunit during the final stages of maturation. Our results provide a structural framework for the coordination of the final maturation events that drive a pre-40S particle toward the mature form capable of engaging in translation.
Validation Report
SummaryFull reportAbout validation report
History
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

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Assembly

Deposited unit
b: 40S ribosomal protein S27-A
c: 40S ribosomal protein S28-A
d: 40S ribosomal protein S29-A
e: 40S ribosomal protein S30-A
g: Guanine nucleotide-binding protein subunit beta-like protein
h: Pre-rRNA-processing protein PNO1
i: Essential nuclear protein 1
j: Protein LTV1
k: Ribosome biogenesis protein TSR1
l: Serine/threonine-protein kinase RIO2
2: 20S ribosomal RNA
A: 40S ribosomal protein S0-A
B: 40S ribosomal protein S1-A
C: 40S ribosomal protein S2
D: 40S ribosomal protein S3
E: 40S ribosomal protein S4-A
F: 40S ribosomal protein S5
G: 40S ribosomal protein S6-A
H: 40S ribosomal protein S7-A
I: 40S ribosomal protein S8-A
J: 40S ribosomal protein S9-A
L: 40S ribosomal protein S11-A
M: 40S ribosomal protein S12
N: 40S ribosomal protein S13
O: 40S ribosomal protein S14-A
P: 40S ribosomal protein S15
Q: 40S ribosomal protein S16-A
R: 40S ribosomal protein S17-A
S: 40S ribosomal protein S18-A
T: 40S ribosomal protein S19-A
U: 40S ribosomal protein S20
V: 40S ribosomal protein S21-A
W: 40S ribosomal protein S22-A
X: 40S ribosomal protein S23-A
Y: 40S ribosomal protein S24-A
Z: 40S ribosomal protein S25-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,411,96484
Polymers1,410,71536
Non-polymers1,24948
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area184540 Å2
ΔGint-1678 kcal/mol
Surface area471330 Å2
MethodPISA

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Components

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40S ribosomal protein ... , 29 types, 29 molecules bcdeABCDEFGHIJLMNOPQRSTUVWXYZ

#1: Protein 40S ribosomal protein S27-A / Ribosome / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8893.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P35997
#2: Protein 40S ribosomal protein S28-A / Ribosome / S33 / Small ribosomal subunit protein eS28-A / YS27


Mass: 7605.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q3E7X9
#3: Protein 40S ribosomal protein S29-A / Ribosome / S36 / Small ribosomal subunit protein uS14-A / YS29


Mass: 6675.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P41057
#4: Protein 40S ribosomal protein S30-A / Ribosome / Small ribosomal subunit protein eS30-A


Mass: 7137.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX33
#12: Protein 40S ribosomal protein S0-A / Ribosome / Nucleic acid-binding protein NAB1A / Small ribosomal subunit protein uS2-A


Mass: 28083.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P32905
#13: Protein 40S ribosomal protein S1-A / Ribosome / RP10A / Small ribosomal subunit protein eS1-A


Mass: 28798.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P33442
#14: Protein 40S ribosomal protein S2 / / Omnipotent suppressor protein SUP44 / RP12 / S4 / Small ribosomal subunit protein uS5 / YS5


Mass: 27490.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P25443
#15: Protein 40S ribosomal protein S3 / / RP13 / Small ribosomal subunit protein uS3 / YS3


Mass: 26542.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05750
#16: Protein 40S ribosomal protein S4-A / Ribosome / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6


Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX35
#17: Protein 40S ribosomal protein S5 / / RP14 / S2 / Small ribosomal subunit protein uS7 / YS8


Mass: 25072.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P26783
#18: Protein 40S ribosomal protein S6-A / Ribosome / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4


Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX37
#19: Protein 40S ribosomal protein S7-A / Ribosome / RP30 / RP40 / Small ribosomal subunit protein eS7-A


Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P26786
#20: Protein 40S ribosomal protein S8-A / Ribosome / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9


Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX39
#21: Protein 40S ribosomal protein S9-A / Ribosome / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: O13516
#22: Protein 40S ribosomal protein S11-A / Ribosome / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12


Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX47
#23: Protein 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 15488.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P48589
#24: Protein 40S ribosomal protein S13 / / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05756
#25: Protein 40S ribosomal protein S14-A / Ribosome / RP59A / Small ribosomal subunit protein uS11-A


Mass: 14562.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P06367
#26: Protein 40S ribosomal protein S15 / / RIG protein / RP52 / S21 / Small ribosomal subunit protein uS19 / YS21


Mass: 16031.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q01855
#27: Protein 40S ribosomal protein S16-A / Ribosome / RP61R / Small ribosomal subunit protein uS9-A


Mass: 15877.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX51
#28: Protein 40S ribosomal protein S17-A / Ribosome / RP51A / Small ribosomal subunit protein eS17-A


Mass: 15820.413 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P02407
#29: Protein 40S ribosomal protein S18-A / Ribosome / Small ribosomal subunit protein uS13-A


Mass: 17071.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX55
#30: Protein 40S ribosomal protein S19-A / Ribosome / RP55A / S16a / Small ribosomal subunit protein eS19-A / YP45 / YS16A


Mass: 15942.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P07280
#31: Protein 40S ribosomal protein S20 / / Small ribosomal subunit protein uS10


Mass: 13929.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38701
#32: Protein 40S ribosomal protein S21-A / Ribosome / S26 / Small ribosomal subunit protein eS21-A / YS25


Mass: 9758.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0C0V8
#33: Protein 40S ribosomal protein S22-A / Ribosome / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22


Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0C0W1
#34: Protein 40S ribosomal protein S23-A / Ribosome / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX29
#35: Protein 40S ribosomal protein S24-A / Ribosome / RP50 / Small ribosomal subunit protein eS24-A


Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX31
#36: Protein 40S ribosomal protein S25-A / Ribosome / RP45 / S31 / Small ribosomal subunit protein eS25-A / YS23


Mass: 12067.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q3E792

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Protein , 6 types, 6 molecules ghijkl

#5: Protein Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ...Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ribosomal subunit protein RACK1


Mass: 34841.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38011
#6: Protein Pre-rRNA-processing protein PNO1 / Partner of NOB1 / Ribosomal RNA-processing protein 20


Mass: 30380.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q99216
#7: Protein Essential nuclear protein 1


Mass: 55207.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38333
#8: Protein Protein LTV1 / Low-temperature viability protein 1


Mass: 53463.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P34078
#9: Protein Ribosome biogenesis protein TSR1 / / 20S rRNA accumulation protein 1


Mass: 90876.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q07381
#10: Protein Serine/threonine-protein kinase RIO2


Mass: 49192.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40160, non-specific serine/threonine protein kinase

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RNA chain , 1 types, 1 molecules 2

#11: RNA chain 20S ribosomal RNA /


Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 874346701

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Non-polymers , 2 types, 48 molecules

#37: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#38: Chemical...
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: Mg

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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: Cytoplasmic pre-40S ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#36 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
12RELION23D reconstruction
13PHENIX1.9model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 165168 / Symmetry type: POINT

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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