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- PDB-5wyk: Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-dep... -

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Database: PDB / ID: 5wyk
TitleCryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)
Components
  • (40S ribosomal protein ...) x 16
  • (Helical domain ...) x 2
  • (Nucleolar protein ...Nucleolus) x 2
  • (Ribosomal RNA-processing protein ...) x 2
  • (Ribosome biogenesis protein ...) x 2
  • (U3 small nucleolar RNA-associated protein ...) x 6
  • (U3 small nucleolar ribonucleoprotein protein ...) x 2
  • 13 kDa ribonucleoprotein-associated protein
  • 18S ribosomal RNA
  • 5ETS RNA
  • Enp2
  • KRR1 small subunit processome component
  • Mpp10,U3 small nucleolar RNA-associated protein MPP10
  • Periodic tryptophan protein 2
  • Pre-rRNA-processing protein PNO1
  • RNA 3'-terminal phosphate cyclase-like protein
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Sof1
  • U3 RNA
  • Unassigned helices
  • Utp11
  • Utp15
  • Utp17
  • Utp4
  • Utp5
  • Utp7
  • Utp8
  • Utp9
  • rRNA 2'-O-methyltransferase fibrillarin
  • rRNA-processing protein FCF1
KeywordsRIBOSOME / ribosome / 90S / pre-ribosome / protein-RNA complex
Function / homologytRNA methyltransferase complex GCD14 subunit / WD40-repeat-containing domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S7 domain superfamily / K Homology domain, type 1 superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily / Nop domain superfamily / Ribosome biogenesis protein Bms1, N-terminal ...tRNA methyltransferase complex GCD14 subunit / WD40-repeat-containing domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S7 domain superfamily / K Homology domain, type 1 superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily / Nop domain superfamily / Ribosome biogenesis protein Bms1, N-terminal / Ribosomal protein S8 superfamily / Nrap protein, domain 6 / Nrap protein, domain 5 / Nrap protein, domain 4 / Nrap protein, domain 3 / Nrap protein, domain 2 / rRNA-processing protein Fcf1, PIN domain / Ribosomal protein S4e, central domain superfamily / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 / RNA 3'-terminal phosphate cyclase / Ribosomal S3Ae family / Ribosomal family S4e / Ribosomal protein L1p/L10e family / KOW motif / Ribosomal protein S11 / WD domain, G-beta repeat / ATPase family associated with various cellular activities (AAA) / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / Nrap protein domain 1 / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S8e / Ribosomal protein S9, conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / U3 small nucleolar RNA-associated protein 10 / HEAT, type 2 / Fibrillarin, conserved site / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S15P / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / WD40 repeat, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S8e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L1-like / Bms1/Tsr1-type G domain / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / S-adenosyl-L-methionine-dependent methyltransferase / PIN-like domain superfamily / Alpha/beta knot methyltransferases / tRNA (guanine-N1-)-methyltransferase, N-terminal / Helix hairpin bin domain superfamily / Ribosomal protein L1/ribosomal biogenesis protein / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / P-loop containing nucleoside triphosphate hydrolase / Periodic tryptophan protein 2 / Anaphase-promoting complex subunit 4, WD40 domain / Ribosomal RNA-processing protein 7 / Ribosomal RNA assembly KRR1 / Ribosomal protein S28e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal S11, conserved site / Ribosomal protein S28e signature. / HEAT repeat profile. / RNA 3'-terminal phosphate cyclase signature. / Ribosomal protein S8e signature. / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein L7Ae signature. / Ribosomal protein S7e signature. / Trp-Asp (WD) repeats circular profile. / Trp-Asp (WD) repeats signature. / Ribosomal protein S4 signature. / Fibrillarin signature. / Ribosomal protein S24e signature. / Ribosomal protein S4e signature. / Ribosomal protein S15 signature. / Trp-Asp (WD) repeats profile. / Brix domain profile. / Ribosomal protein S17 signature. / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Processing of Intronless Pre-mRNAs / GTP hydrolysis and joining of the 60S ribosomal subunit / Ribosomal scanning and start codon recognition / Formation of the ternary complex, and subsequently, the 43S complex / mRNA Splicing - Minor Pathway
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.5 Å resolution
AuthorsYe, K. / Zhu, X. / Sun, Q.
CitationJournal: Elife / Year: 2017
Title: Molecular architecture of the 90S small subunit pre-ribosome.
Authors: Qi Sun / Xing Zhu / Jia Qi / Weidong An / Pengfei Lan / Dan Tan / Rongchang Chen / Bing Wang / Sanduo Zheng / Cheng Zhang / Xining Chen / Wei Zhang / Jing Chen / Meng-Qiu Dong / Keqiong Ye
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 13, 2017 / Release: Mar 29, 2017
RevisionDateData content typeGroupProviderType
1.0Mar 29, 2017Structure modelrepositoryInitial release
1.1May 17, 2017Structure modelStructure summary

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
3A: U3 RNA
3B: rRNA 2'-O-methyltransferase fibrillarin
3C: rRNA 2'-O-methyltransferase fibrillarin
3D: Nucleolar protein 56
3E: Nucleolar protein 58
3F: Ribosomal RNA-processing protein 9
3G: 13 kDa ribonucleoprotein-associated protein
3H: 13 kDa ribonucleoprotein-associated protein
5A: 5ETS RNA
AA: Utp4
AB: Utp5
AC: Utp8
AD: Utp9
AE: U3 small nucleolar RNA-associated protein 10
AF: Utp15
AG: Utp17
B1: Ribosome biogenesis protein BMS1
BA: Periodic tryptophan protein 2
BB: U3 small nucleolar RNA-associated protein 12
BC: U3 small nucleolar RNA-associated protein 13
BD: U3 small nucleolar RNA-associated protein 18
BE: U3 small nucleolar RNA-associated protein 21
CA: Ribosomal RNA-processing protein 7
CB: U3 small nucleolar RNA-associated protein 22
E1: Ribosomal RNA small subunit methyltransferase NEP1
E2: Ribosomal RNA small subunit methyltransferase NEP1
E4: Enp2
K1: KRR1 small subunit processome component
MA: U3 small nucleolar ribonucleoprotein protein IMP3
MB: U3 small nucleolar ribonucleoprotein protein IMP4
MC: Mpp10,U3 small nucleolar RNA-associated protein MPP10
P1: Pre-rRNA-processing protein PNO1
R1: RNA 3'-terminal phosphate cyclase-like protein
S1: Sof1
SA: 18S ribosomal RNA
SC: 40S ribosomal protein S1-A
SF: 40S ribosomal protein S4-A
SG: 40S ribosomal protein S5
SI: 40S ribosomal protein S7-A
SJ: 40S ribosomal protein S8-A
SK: 40S ribosomal protein S9-A
SM: 40S ribosomal protein S11-A
SO: 40S ribosomal protein S13
SP: 40S ribosomal protein S14-A
SR: 40S ribosomal protein S16-A
SX: 40S ribosomal protein S22-A
SY: 40S ribosomal protein S23-A
SZ: 40S ribosomal protein S24-A
Sc: 40S ribosomal protein S27-A
Sd: 40S ribosomal protein S28-A
Sf: 40S ribosomal protein S30-A
U1: Utp7
U2: Utp11
U4: rRNA-processing protein FCF1
U5: Ribosome biogenesis protein UTP30
UA: Helical domain protein
UB: Helical domain protein
UC: Unassigned helices


Theoretical massNumber of molelcules
Total (without water)3,618,02458
Polyers3,618,02458
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules 3A5ASA

#1: RNA chain U3 RNA


Mass: 106503.258 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#7: RNA chain 5ETS RNA


Mass: 225543.094 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: GenBank: 1262303
#32: RNA chain 18S ribosomal RNA /


Mass: 583636.562 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: GenBank: 874346701

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Protein/peptide , 20 types, 23 molecules 3B3C3G3HAAABACADAFAGBAE1E2E4K1MCP1R1S1U1U2U4UC

#2: Protein/peptide rRNA 2'-O-methyltransferase fibrillarin / Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA-associated protein NOP1


Mass: 34525.418 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P15646, Methyltransferases
#6: Protein/peptide 13 kDa ribonucleoprotein-associated protein / Small nuclear ribonucleoprotein-associated protein 1


Mass: 13582.855 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P39990
#8: Protein/peptide Utp4


Mass: 66059.172 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#9: Protein/peptide Utp5


Mass: 54740.609 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#10: Protein/peptide Utp8


Mass: 60697.750 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#11: Protein/peptide Utp9


Mass: 48953.438 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#13: Protein/peptide Utp15 /


Mass: 43676.871 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#14: Protein/peptide Utp17


Mass: 76271.414 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#16: Protein/peptide Periodic tryptophan protein 2 / U three protein 1 / U3 small nucleolar RNA-associated protein 1 / U3 snoRNA-associated protein 1


Mass: 104097.039 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25635
#23: Protein/peptide Ribosomal RNA small subunit methyltransferase NEP1 / / 18S rRNA (pseudouridine(1189)-N1)-methyltransferase / 18S rRNA Psi1189 methyltransferase / Essential for mitotic growth protein 1 / Nucleolar essential protein 1


Mass: 27936.461 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: Q06287, rRNA small subunit pseudouridine methyltransferase Nep1
#24: Protein/peptide Enp2


Mass: 60187.137 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#25: Protein/peptide KRR1 small subunit processome component / / KRR-R motif-containing protein 1 / Ribosomal RNA assembly protein KRR1


Mass: 37226.254 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25586
#28: Protein/peptide Mpp10,U3 small nucleolar RNA-associated protein MPP10 / U3 snoRNA-associated protein MPP10 / M phase phosphoprotein 10


Mass: 54936.984 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P47083
#29: Protein/peptide Pre-rRNA-processing protein PNO1 / Partner of NOB1 / Ribosomal RNA-processing protein 20


Mass: 30380.623 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q99216
#30: Protein/peptide RNA 3'-terminal phosphate cyclase-like protein


Mass: 40220.559 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08096
#31: Protein/peptide Sof1


Mass: 41634.328 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#49: Protein/peptide Utp7


Mass: 47166.211 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#50: Protein/peptide Utp11


Mass: 21294.152 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#51: Protein/peptide rRNA-processing protein FCF1 / FAF1-copurifying factor 1


Mass: 21650.729 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q05498
#55: Protein/peptide Unassigned helices


Mass: 87930.383 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Nucleolar protein ... , 2 types, 2 molecules 3D3E

#3: Protein/peptide Nucleolar protein 56 / Nucleolus / Ribosome biosynthesis protein SIK1 / Suppressor of I kappa b protein 1


Mass: 56961.152 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12460
#4: Protein/peptide Nucleolar protein 58 / Nucleolus / Nucleolar protein 5


Mass: 57060.344 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12499

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Ribosomal RNA-processing protein ... , 2 types, 2 molecules 3FCA

#5: Protein/peptide Ribosomal RNA-processing protein 9


Mass: 65146.969 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06506
#21: Protein/peptide Ribosomal RNA-processing protein 7


Mass: 34526.441 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25368

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U3 small nucleolar RNA-associated protein ... , 6 types, 6 molecules AEBBBCBDBECB

#12: Protein/peptide U3 small nucleolar RNA-associated protein 10 / U3 snoRNA-associated protein 10 / U three protein 10 / U3 protein 10 required for transcription / t-UTP10


Mass: 200298.984 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P42945
#17: Protein/peptide U3 small nucleolar RNA-associated protein 12 / U3 snoRNA-associated protein 12 / DOM34-interacting protein 2 / U three protein 12


Mass: 106481.133 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12220
#18: Protein/peptide U3 small nucleolar RNA-associated protein 13 / U3 snoRNA-associated protein 13 / U three protein 13


Mass: 91132.562 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q05946
#19: Protein/peptide U3 small nucleolar RNA-associated protein 18 / U3 snoRNA-associated protein 18 / U three protein 18


Mass: 66494.250 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40362
#20: Protein/peptide U3 small nucleolar RNA-associated protein 21 / U3 snoRNA-associated protein 21 / U three protein 21


Mass: 104927.844 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06078
#22: Protein/peptide U3 small nucleolar RNA-associated protein 22 / U3 snoRNA-associated protein 22 / U three protein 22


Mass: 140660.141 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53254

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Ribosome biogenesis protein ... , 2 types, 2 molecules B1U5

#15: Protein/peptide Ribosome biogenesis protein BMS1 /


Mass: 135792.281 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08965
#52: Protein/peptide Ribosome biogenesis protein UTP30 / / U3 snoRNP-associated protein UTP30


Mass: 31668.939 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36144

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U3 small nucleolar ribonucleoprotein protein ... , 2 types, 2 molecules MAMB

#26: Protein/peptide U3 small nucleolar ribonucleoprotein protein IMP3 / U3 snoRNP protein IMP3 / Interacting with MPP10 protein 3


Mass: 21928.529 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32899
#27: Protein/peptide U3 small nucleolar ribonucleoprotein protein IMP4 / U3 snoRNP protein IMP4 / Interacting with MPP10 protein 4


Mass: 33536.168 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53941

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40S ribosomal protein ... , 16 types, 16 molecules SCSFSGSISJSKSMSOSPSRSXSYSZScSdSf

#33: Protein/peptide 40S ribosomal protein S1-A / Ribosome / RP10A


Mass: 28798.467 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33442
#34: Protein/peptide 40S ribosomal protein S4-A / Ribosome / RP5 / S7 / YS6


Mass: 29469.330 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX35
#35: Protein/peptide 40S ribosomal protein S5 / / RP14 / S2 / YS8


Mass: 25072.600 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26783
#36: Protein/peptide 40S ribosomal protein S7-A / Ribosome / RP30 / RP40


Mass: 21658.209 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26786
#37: Protein/peptide 40S ribosomal protein S8-A / Ribosome / RP19 / S14 / YS9


Mass: 22537.803 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX39
#38: Protein/peptide 40S ribosomal protein S9-A / Ribosome / RP21 / S13 / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: O13516
#39: Protein/peptide 40S ribosomal protein S11-A / Ribosome / RP41 / S18 / YS12


Mass: 17785.934 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX47
#40: Protein/peptide 40S ribosomal protein S13 / / S27a / YS15


Mass: 17059.945 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05756
#41: Protein/peptide 40S ribosomal protein S14-A / Ribosome / RP59A


Mass: 14562.655 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P06367
#42: Protein/peptide 40S ribosomal protein S16-A / Ribosome / RP61R


Mass: 15877.490 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX51
#43: Protein/peptide 40S ribosomal protein S22-A / Ribosome / RP50 / S24 / YP58 / YS22


Mass: 14650.062 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0W1
#44: Protein/peptide 40S ribosomal protein S23-A / Ribosome / RP37 / S28 / YS14


Mass: 16073.896 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX29
#45: Protein/peptide 40S ribosomal protein S24-A / Ribosome / RP50


Mass: 15362.848 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX31
#46: Protein/peptide 40S ribosomal protein S27-A / Ribosome / RP61 / YS20


Mass: 8893.391 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P35997
#47: Protein/peptide 40S ribosomal protein S28-A / Ribosome / S33 / YS27


Mass: 7605.847 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q3E7X9
#48: Protein/peptide 40S ribosomal protein S30-A / Ribosome


Mass: 7137.541 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX33

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Helical domain ... , 2 types, 2 molecules UAUB

#53: Protein/peptide Helical domain protein


Mass: 137462.422 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#54: Protein/peptide Helical domain protein


Mass: 84015.695 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Details

Sequence details(1) For chains AA, AB, AC, AD, AF, AG, E4, S1, U1 and U2, The authors know the sequences, but they ...(1) For chains AA, AB, AC, AD, AF, AG, E4, S1, U1 and U2, The authors know the sequences, but they were unable to assign the sequences to the coordinates. The correct sequences are as follows. chain AA (UNP Q06679 1-776) MSSSLLSVLKEKSRSLKIRNKPVKMTSQERMIVHRCRFVDFTPATITSLAFSHKSNINKLTPSDLRLAIGRSNGNIEIWNPRNNWFQEMVIEGGKDRSIEGLCWSNVNGESLRLFSIGGSTVVTEWDLATGLPLRNYDCNSGVIWSISINDSQDKLSVGCDNGTVVLIDISGGPGVLEHDTILMRQEARVLTLAWKKDDFVIGGCSDGRIRIWSAQKNDENMGRLLHTMKVDKAKKESTLVWSVIYLPRTDQIASGDSTGSIKFWDFQFATLNQSFKAHDADVLCLTTDTDNNYVFSAGVDRKIFQFSQNTNKSQKNNRWVNSSNRLLHGNDIRAICAYQSKGADFLVSGGVEKTLVINSLTSFSNGNYRKMPTVEPYSKNVLVNKEQRLVVSWSESTVKIWTMGTDSSTEQNYKLVCKLTLKDDQNISTCSLSPDGQVLVVGRPSTTKVFHLQPVGNKLKVTKLDNDLLLRTSTKLVKFIDNSKIVICSCEDDVFIVDLESEEDEKPQEVELLEVTSTKSSIKVPYINRINHLEVDQNIAVISRGCGVVDILDLKARISKPLARLNNFITAVHINTSRKSVVVITADNKIYEFNMNLNSEAENEDSESVLTQWSKNNTDNLPKEWKTLKENCVGIFSDIENSSRLWFWGATWISRIDFDVDFPINKRRKQKKRTHEGLTITDESNFMNDEEDDEDDDIDMEISENLNVLLNQGNKIKSTDVQRNEESSGHFFFTDKYKPLLFVDLISSNELAIIERNPLTFHSKQKAFIQPKLVF chain AB (UNP Q04177 1-643) MDSPVLQSAYDPSGQYLCYVTVALDKQRVGVQPTQRATSSGVDTVWNENFLYLEDSKLKVTCLKWVNLASSDTVAIILGMNNGEIWLYSVLANEVTYKFTTGNSYEIKDIDLMGNQLWCIDSSDAFYQFDLLQFKLLQHFRINNCVQLNKLTIVPAGDSVAQLLVASHSISLIDIEEKKVVMTFPGHVSPVSTLQVITNEFFISGAEGDRFLNVYDIHSGMTKCVLVAESDIKELSHSGQADSIAVTTEDGSLEIFVDPLVSSSTKKRGNKSKKSSKKIQIVSKDGRKVPIYNAFINKDLLNVSWLQNATMPYFKNLQWREIPNEYTVEISLNWNNKNKSADRDLHGKDLASATNYVEGNARVTSGDNFKHVDDAIKSWERELTSLEQEQAKPPQANELLTETFGDKLESSTVARISGKKTNLKGSNLKTATTTGTVTVILSQALQSNDHSLLETVLNNRDERVIRDTIFRLKPALAVILLERLAERIARQTHRQGPLNVWVKWCLIIHGGYLVSIPNLMSTLSSLHSTLKRRSDLLPRLLALDARLDCTINKFKTLNYEAGDIHSSEPVVEEDEDDVEYNEELDDAGLIEDGEESYGSEEEEEGDSDNEEEQKHTSSKQDGRLETEQSDGEEEAGYSDVEME chain AC (UNP P53276 1-713) MPSLSQPFRLATLPKIASLSNFSLQADYVQVADGTFNESTNNITLGISGSSISQYIINPTPKLTFDYPIPSTNIITACNAEKGQANIDGNIEASTDDEANNEKTINTQKKRNVEIWAFGLMVNKGNYTLNVITKALEDTTDTSNDHLSESDIDNKAYTGSDEFLSQYKIKAKAKVMSIKIDTKNSLVIAILQNGLIEIFDFKLTLLHSFDISYDNLKYAKWFTENGTEYVFVLCPLQDDKVCYKLLELTDCGSGESSPIKELSSTIIEGFSFENSKLCYQFGKLYKLNQGKIYIYSLPHCQLQQVIEFPMVDKLSPGDDLISFQPVSVNRVLLTVNNVIYLLDLLHCSTLSQRELTHVKTFQLLKSAVINSEKSHNSKTIAIGISTKNGPNPTSSLEIINIDVGTNTLKDSLGKSFQVGNNDSSVILKPLFDDKDINDKRVKCNDVSGDSSVPVLHCNEVIEKLSALQDNDITSFDDIFFKELKIKEEHYTEKDRYISDPGFLNKVLDLIFGKFSGNDYPKTLTFLLTHPLFPLSRTRNLLSLLRDQPRLFKQAIVTCPNLPLNELLEELFSIRNRELLLDISFRILQDFTRDSIKQEMKKLSKLDVQNFIEFITSGGEDSSPECFNPSQSTQLFQLLSLVLDSIGLFSLEGALLENLTLYIDKQVEIAERNTELWNLIDTKGFQHGFASSTFDNGTSQKRALPTYTMEYLDI chain AD (UNP P38882 1-575) MGSSLDLVASFSHDSTRFAFQASVAQKNNVDIYPLNETKDYVVNSSLVSHIDYETNDMKVSDVIFFGWCSDLIDTQSSNIKRKLDEDEGTGESSEQRCENFFVNGFPDGRIVVYSSNGKDIVNIIKNKKEILGADTDESDIWILDSDKVVKKLQYNNSKPLKTFTLVDGKDDEIVHFQILHQNGTLLVCIITKQMVYIVDPSKRRPSTKYSFEISDAVACEFSSDGKYLLIANNEELIAYDLKEDSKLIQSWPVQVKTLKTLDDLIMALTTDGKINNYKIGEADKVCSIVVNEDLEIIDFTPINSKQQVLISWLNVNEPNFESISLKEIETQGYITINKNEKNNADEADQKKLEEKEEEAQPEVQHEKKETETKINKKVSKSDQVEIANILSSHLEANSTEILDDLMSGSWTEPEIKKFILTKINTVDHLSKIFLTISKSITQNPWNEENLLPLWLKWLLTLKSGELNSIKDKHTKKNCKHLKSALRSSEEILPVLLGIQGRLEMLRRQAKLREDLAQLSMQEGEDDEIEVIEHSNVISNPLQDQASPVEKLEPDSIVYANGESDEFVDASEYKD chain AF (UNP Q04305 1-513) MSTARPRIITSKAPLLPQQTTPEQRYWRQYTSAQLVKEHNSVTHISFNPQHPHDFAVTSSTRVQIFSSRTRQVIKTFSRFKDVVYSASFRSDGKLLCAGDATGLVSVYDSYNPRTILLSINASTHPTHVTKFHTQDNKILATASDDRVTRLWDISNAYEPQLELTGATDYVRTLSFIPAAPHLVATGSYDGLIRLYDTRSSGSTPIYSLNHDQPVENVIAVSPTQIVSCGGNNFKVWDLTSNKKLYERGNFNKAVTCLDYVENFDSPMQSALIASSLDGHVKVFDPLDNFQVKFGWKFSGPVLSCAVSPSTAQGNRHLVAGLSSGLLAIRTKKKEKRSSDKENAPASFNKNAKSNNFQRMMRGSEYQGDQEHIIHNDKVRSQRRMRAFERNINQFKWSEALDNAFVPGMAKELTLTVLQELRKRGKVRVALYGRDESTLEPLLNWCLKGIEDVRSASIVADWVAVVLELYGNTLESSPVLQELMIDLKTKVRHEIHKSKEAQRIEGMLQLLTS chain AG (UNP Q02931 1-896) MTQSLGIEQYKLSVVSGGKPALNNLSSVTGNKNIARLSQDQRNYIIPFNNQIKVYSVETRQCVKTLKFANNSLLSGIFLQEEENNESIVKILLGDITVPQQEDAHLITVFTNNGHVIVLNYKGKLVESPKHFKISLADEKLANVFHSEGNYRILTTFKDPSQKAHNSLQSYRLYALTFDDAKKQFEVAHQAEWHNVILSNISSNGKLLAHMCKDVSTKDHEHKSISVVSLFDDSVNLSFPLGSILSSQTQSLSYNTRYVSSMAIDNMGQQLAVGFASGVISIVSLADLQIRLLKWHIDSVLSLSFSHDGSYLLSGGWEKVMSLWQLETNSQQFLPRLNGIIIDCQVLGPQGNYYSLILQMTENNSNSDYQFLLLNASDLTSKLSINGPLPVFNSTIKHIQQPISAMNTKNSNSITSLNHSKKKQSRKLIKSRRQDFTTNVEINPINKNLYFPHISAVQIFDFYKNEQVNYQYLTSGVNNSMGKVRFELNLQDPIITDLKFTKDGQWMITYEIEYPPNDLLSSKDLTHILKFWTKNDNETNWNLKTKVINPHGISVPITKILPSPRSVNNSQGCLTADNNGGLKFWSFDSHESNWCLKKISLPNFNHFSNSVSLAWSQDGSLIFHGFDDKLQILDFDTFKKFESLENTKTVSEFTLDSEIQTVKLINDTNLIVATRTTLNAINLLRGQVINSFDLYPFVNGVYKNGHMDRLITCDERTGNIALVINQQLTDLDGVPTINYKSRIIIFDSDLSTKLGNFTHHEYISWIGWNYDTDFIFLDIESTLGVVGTTVNTQLSDEVNNEGILDGLVSNTITTSASNSDIFAEQLHKLSSRGKKSDTRDKNTNDNDEDEEDIALEFINGEKKDKLVNMNSFTSMFDNIQNVQMDTFFDRVMKVLT chain E4 (UNP P48234 1-707) MVLKSTSANDVSVYQVSGTNVSRSLPDWIAKKRKRQLKNDLEYQNRVELIQDFEFSEASNKIKVSRDGQYCMATGTYKPQIHVYDFANLSLKFDRHTDAENVDFTILSDDWTKSVHLQNDRSIQFQNKGGLHYTTRIPKFGRSLVYNKVNCDLYVGASGNELYRLNLEKGRFLNPFKLDTEGVNHVSINEVNGLLAAGTETNVVEFWDPRSRSRVSKLYLENNIDNRPFQVTTTSFRNDGLTFACGTSNGYSYIYDLRTSEPSIIKDQGYGFDIKKIIWLDNVGTENKIVTCDKRIAKIWDRLDGKAYASMEPSVDINDIEHVPGTGMFFTANESIPMHTYYIPSLGPSPRWCSFLDSITEELEEKPSDTVYSNYRFITRDDVKKLNLTHLVGSRVLRAYMHGFFINTELYDKVSLIANPDAYKDEREREIRRRIEKERESRIRSSGAVQKPKIKVNKTLVDKLSQKRGDKVAGKVLTDDRFKEMFEDEEFQVDEDDYDFKQLNPVKSIKETEEGAAKRIRALTAAEESDEERIAMKDGRGHYDYEDEESDEEESDDETNQKSNKEELSEKDLRKMEKQKALIERRKKEKEQSERFMNEMKAGTSTSTQRDESAHVTFGEQVGELLEVENGKKSNESILRRNQRGEAELTFIPQRKSKKDGNYKSRRHDNSSDEEGIDENGNKKDNGRSKPRFENRRRASKNAFRGM chain S1 (UNP P33750 1-489) MKIKTIKRSADDYVPVKSTQESQMPRNLNPELHPFERAREYTKALNATKLERMFAKPFVGQLGYGHRDGVYAIAKNYGSLNKLATGSADGVIKYWNMSTREEFVSFKAHYGLVTGLCVTQPRFHDKKPDLKSQNFMLSCSDDKTVKLWSINVDDYSNKNSSDNDSVTNEEGLIRTFDGESAFQGIDSHRENSTFATGGAKIHLWDVNRLKPVSDLSWGADNITSLKFNQNETDILASTGSDNSIVLYDLRTNSPTQKIVQTMRTNAICWNPMEAFNFVTANEDHNAYYYDMRNLSRSLNVFKDHVSAVMDVDFSPTGDEIVTGSYDKSIRIYKTNHGHSREIYHTKRMQHVFQVKYSMDSKYIISGSDDGNVRLWRSKAWERSNVKTTREKNKLEYDEKLKERFRHMPEIKRISRHRHVPQVIKKAQEIKNIELSSIKRREANERRTRKDMPYISERKKQIVGTVHKYEDSGRDRKRRKEDDKRDTQEK chain U1 (UNP P40055 1-554) MGHKKNGHRRQIKERENQNKFERSTYTNNAKNNHTQTKDKKLRAGLKKIDEQYKKAVSSAAATDYLLPESNGYLEPENELEKTFKVQQSEIKSSVDVSTANKALDLSLKEFGPYHIKYAKNGTHLLITGRKGHVASMDWRKGQLRAELFLNETCHSATYLQNEQYFAVAQKKYTFIYDHEGTELHRLKQHIEARHLDFLPYHYLLVTAGETGWLKYHDVSTGQLVSELRTKAGPTMAMAQNPWNAVMHLGHSNGTVSLWSPSMPEPLVKLLSARGPVNSIAIDRSGYYMATTGADRSMKIWDIRNFKQLHSVESLPTPGTNVSISDTGLLALSRGPHVTLWKDALKLSGDSKPCFGSMGGNPHRNTPYMSHLFAGNKVENLGFVPFEDLLGVGHQTGITNLIVPGAGEANYDALELNPFETKKQRQEQEVRTLLNKLPADTITLDPNSIGSVDKRSSTIRLNAKDLAQTTMDANNKAKTNSDIPDVKPDVKGKNSGLRSFLRKKTQNVIDERKLRVQKQLDKEKNIRKRNHQIKQGLISEDHKDVIEEALSRFG chain U2 (UNP P34247 1-250) MAKLVHDVQKKQHRERSQLTSRSRYGFLEKHKDYVKRAQDFHRKQSTLKVLREKAKERNPDEYYHAMHSRKTDAKGLLISSRHGDEEDESLSMDQVKLLKTQDSNYVRTLRQIELKKLEKGAKQLMFKSSGNHTIFVDSREKMNEFTPEKFFNTTSEMVNRSENRLTKDQLAQDISNNRNASSIMPKESLDKKKLKKFKQVKQHLQRETQLKQVQQRMDAQRELLKKGSKKKIVDSSGKISFKWKKQRKR (2) For chain MC Authors know the sequence and partially assigned the sequence (429-593) to the coordinates. The correct sequences are as follows. chain MC (UNP P47083 1-593) MSELFGVLKSNAGRIILKDPSATSKDVKAYIDSVINTCKNGSITKKAELDEITVDGLDANQVWWQVKLVLDSIDGDLIQGIQELKDVVTPSHNLSDGSTLNSSSGEESELEEAESVFKEKQMLSADVSEIEEQSNDSLSENDEEPSMDDEKTSAEAAREEFAEEKRISSGQDERHSSPDPYGINDKFFDLEKFNRDTLAAEDSNEASEGSEDEDIDYFQDMPSDDEEEEAIYYEDFFDKPTKEPVKKHSDVKDPKEDEELDEEEHDSAMDKVKLDLFADEEDEPNAEGVGEASDKNLSSFEKQQIEIRKQIEQLENEAVAEKKWSLKGEVKAKDRPEDALLTEELEFDRTAKPVPVITSEVTESLEDMIRRRIQDSNFDDLQRRTLLDITRKSQRPQFELSDVKSSKSLAEIYEDDYTRAEDESALSEELQKAHSEISELYANLVYKLDVLSSVHFVPKPASTSLEIRVETPTISMEDAQPLYMSNASSLAPQEIYNVGKAEKDGEIRLKNGVAMSKEELTREDKNRLRRALKRKRSKANLPNVNKRSKRNDVVDTLSKAKNITVINQKGEKKDVSGKTKKSRSGPDSTNIKL (3) For chains UA, UB and UC The authors don't know the sequence.

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)
Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer ID
1100 mMpotassium acetateCH3COOK1
220 mMHEPES-KHEPES-K1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins / Details: blot for 2 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 / Calibrated magnification: 79545 / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.6 sec. / Electron dose: 40 e/Å2 / Film or detector model: OTHER / Number of grids imaged: 1 / Number of real images: 1102
Image scansWidth: 4000 / Height: 4000

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Processing

EM software
IDNameVersionCategory
2Serial EMimage acquisition
4CTFFIND4CTF correction
10Relion1.4initial Euler assignment
11Relion1.4final Euler assignment
12Relion1.4classification
13Relion1.43D reconstruction
Image processingDetails: detector is Falcon III
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNumber of particles selected: 195317
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 73543 / Number of class averages: 1 / Symmetry type: POINT

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