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- PDB-6ft6: Structure of the Nop53 pre-60S particle bound to the exosome nucl... -

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Entry
Database: PDB / ID: 6ft6
TitleStructure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors
Components
  • (60S ribosomal protein ...) x 35
  • (Exosome complex ...) x 2
  • (Nucleolar GTP-binding protein ...) x 2
  • (Ribosome assembly ...) x 2
  • (Ribosome biogenesis protein ...) x 3
  • 25S ribosomal RNA
  • 5S ribosomal RNA
  • 7S ribosomal RNA
  • ATP-dependent RNA helicase DOB1
  • Bud site selection protein 20
  • Eukaryotic translation initiation factor 6
  • MPP6
  • Nuclear GTP-binding protein NUG1
  • Pescadillo homolog
  • Probable metalloprotease ARX1
  • Regulator of ribosome biosynthesis
  • UPF0642 protein YBL028C
  • rRNA-processing protein CGR1
KeywordsRNA / RNA exosome / Ribosome / pre-ribosome / Mtr4 / Helicase
Function / homologyNOG1 N-terminal helical domain / Ribosomal protein L22e superfamily / Ribosomal protein L7/L30 / Ribosomal protein L14 / 60S ribosomal protein L19 / Ribosomal biogenesis NSA2 family / Ribosomal protein L30/YlxQ / Ribosomal protein L35A superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily ...NOG1 N-terminal helical domain / Ribosomal protein L22e superfamily / Ribosomal protein L7/L30 / Ribosomal protein L14 / 60S ribosomal protein L19 / Ribosomal biogenesis NSA2 family / Ribosomal protein L30/YlxQ / Ribosomal protein L35A superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L7A/L8 superfamily / 60S ribosomal protein L10P, insertion domain / Ribosomal protein L38e superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / BRCT domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosome biogenesis protein Rpf2 / Ribosomal Proteins L2, RNA binding domain / WD40-repeat-containing domain superfamily / Metallopeptidase family M24 / Ribosomal protein L21e / Ribosomal L39 protein / Ribosomal L29 protein / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L15 / ribosomal L5P family C-terminus / Ribosomal protein L4/L1 family / Ribosomal protein L13 / HRDC domain / KOW motif / Ribosomal protein L22p/L17e / Ribosomal protein L10 / WD domain, G-beta repeat / Ribosomal protein L6 / Ribosomal protein L30p/L7e / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Helicase conserved C-terminal domain / DEAD/DEAH box helicase / Ribosomal protein L14p/L23e / Ribosomal protein L32e superfamily / Zinc finger C2H2 superfamily / Ribosomal protein L6e / 60S ribosomal protein L18a/ L20, eukaryotes / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / Zinc finger, double-stranded RNA binding / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein L18e, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L18e/L15P / Ribosomal protein L5, conserved site / Ribosomal protein L15e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein L39e, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L14P, conserved site / Ribosomal protein L3, conserved site / WD40 repeat, conserved site / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L15 / Ribosomal protein L29/L35 superfamily / Creatinase/aminopeptidase-like / Ribosomal protein L19/L19e superfamily / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosome assembly factor Mrt4 / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / OBG-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein L31e domain superfamily / 50S ribosomal protein L30e-like / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / P-loop containing nucleoside triphosphate hydrolase / 60S ribosomal protein L4, C-terminal domain / rRNA-processing arch domain / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Nucleolar GTP-binding protein 2 / Nucleolar GTP-binding protein 1 / Ribosomal protein L15e core domain superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L36e / Ribosomal protein L31e / Ribosomal protein L7Ae/L8/Nhp2 family
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsSchuller, J.M. / Falk, S. / Conti, E.
CitationJournal: Science / Year: 2018
Title: Structure of the nuclear exosome captured on a maturing preribosome.
Authors: Jan Michael Schuller / Sebastian Falk / Lisa Fromm / Ed Hurt / Elena Conti
Abstract: The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex ...The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60) during 7-to-5.8 rRNA processing. The cofactors of the nuclear exosome are sandwiched between the ribonuclease core complex (Exo-10) and the remodeled "foot" structure of the pre-60 particle, which harbors the 5.8 rRNA precursor. The exosome-associated helicase Mtr4 recognizes the preribosomal substrate by docking to specific sites on the 25 rRNA, captures the 3' extension of the 5.8 rRNA, and channels it toward Exo-10. The structure elucidates how the exosome forms a structural and functional unit together with its massive pre-60 substrate to process rRNA during ribosome maturation.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 20, 2018 / Release: Mar 28, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 28, 2018Structure modelrepositoryInitial release
1.1Apr 25, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last
1.2Aug 29, 2018Structure modelData collection / Database referencespdbx_database_related_pdbx_database_related.db_id

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Structure visualization

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Assembly

Deposited unit
2: 7S ribosomal RNA
A: 60S ribosomal protein L2-A
B: 60S ribosomal protein L3
C: 60S ribosomal protein L4-A
D: 60S ribosomal protein L5
E: 60S ribosomal protein L6-A
F: 60S ribosomal protein L7-A
G: 60S ribosomal protein L8-A
H: 60S ribosomal protein L9-A
I: Bud site selection protein 20
J: 60S ribosomal protein L11-A
L: 60S ribosomal protein L13-A
M: 60S ribosomal protein L14-A
N: 60S ribosomal protein L15-A
O: 60S ribosomal protein L16-A
P: 60S ribosomal protein L17-A
Q: 60S ribosomal protein L18-A
R: 60S ribosomal protein L19-A
S: 60S ribosomal protein L20-A
T: 60S ribosomal protein L21-A
U: 60S ribosomal protein L22-A
V: 60S ribosomal protein L23-A
W: Ribosome assembly factor MRT4
X: 60S ribosomal protein L25
Y: 60S ribosomal protein L26-A
Z: 60S ribosomal protein L27-A
a: 60S ribosomal protein L28
b: Nucleolar GTP-binding protein 1
c: 60S ribosomal protein L30
d: 60S ribosomal protein L31-A
e: 60S ribosomal protein L32
f: 60S ribosomal protein L33-A
g: 60S ribosomal protein L34-A
h: 60S ribosomal protein L35-A
i: 60S ribosomal protein L36-A
j: 60S ribosomal protein L37-A
k: 60S ribosomal protein L38
l: 60S ribosomal protein L39
m: Nucleolar GTP-binding protein 2
n: Pescadillo homolog
p: 60S ribosomal protein L43-A
r: Ribosome biogenesis protein NSA2
s: Nuclear GTP-binding protein NUG1
u: Ribosome biogenesis protein RLP24
v: Ribosome biogenesis protein RPF2
w: Regulator of ribosome biosynthesis
x: Ribosome assembly protein 4
y: Eukaryotic translation initiation factor 6
z: UPF0642 protein YBL028C
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: Probable metalloprotease ARX1
5: rRNA-processing protein CGR1
KK: Exosome complex exonuclease RRP6
LL: Exosome complex protein LRP1
MM: ATP-dependent RNA helicase DOB1
NN: MPP6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,670,68665
Polyers2,669,32957
Non-polymers1,3578
Water0
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules 213

#1: RNA chain 7S ribosomal RNA /


Mass: 51999.754 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 1279395616
#50: RNA chain 25S ribosomal RNA /


Mass: 1097493.875 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 834774822
#51: RNA chain 5S ribosomal RNA /


Mass: 38951.105 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 1329886537

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60S ribosomal protein ... , 35 types, 35 molecules ABCDEFGHJLMNOPQRSTUVXYZacdefgh...

#2: Protein/peptide 60S ribosomal protein L2-A / Ribosome / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX45
#3: Protein/peptide 60S ribosomal protein L3 / / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P14126
#4: Protein/peptide 60S ribosomal protein L4-A / Ribosome / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P10664
#5: Protein/peptide 60S ribosomal protein L5 / / L1 / L1a / Large ribosomal subunit protein uL18 / Ribosomal 5S RNA-binding protein / YL3


Mass: 33764.828 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P26321
#6: Protein/peptide 60S ribosomal protein L6-A / Ribosome / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q02326
#7: Protein/peptide 60S ribosomal protein L7-A / Ribosome / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05737
#8: Protein/peptide 60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P17076
#9: Protein/peptide 60S ribosomal protein L9-A / Ribosome / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05738
#11: Protein/peptide 60S ribosomal protein L11-A / Ribosome / L16 / Large ribosomal subunit protein uL5-A / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0C0W9
#12: Protein/peptide 60S ribosomal protein L13-A / Ribosome / Large ribosomal subunit protein eL13-A


Mass: 22604.164 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q12690
#13: Protein/peptide 60S ribosomal protein L14-A / Ribosome / Large ribosomal subunit protein eL14-A


Mass: 15195.066 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P36105
#14: Protein/peptide 60S ribosomal protein L15-A / Ribosome / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05748
#15: Protein/peptide 60S ribosomal protein L16-A / Ribosome / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P26784
#16: Protein/peptide 60S ribosomal protein L17-A / Ribosome / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20589.518 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05740
#17: Protein/peptide 60S ribosomal protein L18-A / Ribosome / Large ribosomal subunit protein eL18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX49
#18: Protein/peptide 60S ribosomal protein L19-A / Ribosome / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX82
#19: Protein/peptide 60S ribosomal protein L20-A / Ribosome / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX23
#20: Protein/peptide 60S ribosomal protein L21-A / Ribosome / Large ribosomal subunit protein eL21-A


Mass: 18279.266 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q02753
#21: Protein/peptide 60S ribosomal protein L22-A / Ribosome / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05749
#22: Protein/peptide 60S ribosomal protein L23-A / Ribosome / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14493.950 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX41
#24: Protein/peptide 60S ribosomal protein L25 / / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P04456
#25: Protein/peptide 60S ribosomal protein L26-A / Ribosome / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14265.784 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05743
#26: Protein/peptide 60S ribosomal protein L27-A / Ribosome / Large ribosomal subunit protein eL27-A


Mass: 15568.360 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0C2H6
#27: Protein/peptide 60S ribosomal protein L28 / / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P02406
#29: Protein/peptide 60S ribosomal protein L30 / / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P14120
#30: Protein/peptide 60S ribosomal protein L31-A / Ribosome / L34 / Large ribosomal subunit protein eL31-A / YL28


Mass: 12980.158 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0C2H8
#31: Protein/peptide 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38061
#32: Protein/peptide 60S ribosomal protein L33-A / Ribosome / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05744
#33: Protein/peptide 60S ribosomal protein L34-A / Ribosome / Large ribosomal subunit protein eL34-A


Mass: 13673.196 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P87262
#34: Protein/peptide 60S ribosomal protein L35-A / Ribosome / Large ribosomal subunit protein uL29-A


Mass: 13942.640 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX84
#35: Protein/peptide 60S ribosomal protein L36-A / Ribosome / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11151.259 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05745
#36: Protein/peptide 60S ribosomal protein L37-A / Ribosome / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P49166
#37: Protein/peptide 60S ribosomal protein L38 / / Large ribosomal subunit protein eL38


Mass: 8845.561 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P49167
#38: Protein/peptide 60S ribosomal protein L39 / / L46 / Large ribosomal subunit protein eL39 / YL40


Mass: 6358.640 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P04650
#41: Protein/peptide 60S ribosomal protein L43-A / Ribosome / L37a / Large ribosomal subunit protein eL43-A / YL35


Mass: 10112.952 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX25

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Protein/peptide , 10 types, 10 molecules Inswyz45MMNN

#10: Protein/peptide Bud site selection protein 20


Mass: 18546.982 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q08004
#40: Protein/peptide Pescadillo homolog / Nucleolar protein 7 / Ribosomal RNA-processing protein 13


Mass: 69984.148 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P53261
#43: Protein/peptide Nuclear GTP-binding protein NUG1 / Nuclear GTPase 1


Mass: 57798.652 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40010
#46: Protein/peptide Regulator of ribosome biosynthesis


Mass: 23001.410 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q08746
#48: Protein/peptide Eukaryotic translation initiation factor 6 / eIF-6


Mass: 26476.605 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q12522
#49: Protein/peptide UPF0642 protein YBL028C


Mass: 12435.429 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38202
#52: Protein/peptide Probable metalloprotease ARX1 / Associated with ribosomal export complex protein 1


Mass: 65290.336 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q03862, Hydrolases
#53: Protein/peptide rRNA-processing protein CGR1 / Coiled-coil growth-regulated protein 1


Mass: 14460.057 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P53188
#56: Protein/peptide ATP-dependent RNA helicase DOB1 / mRNA transport regulator MTR4


Mass: 115230.648 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: MTR4, DOB1, YJL050W, J1158 / Production host: Escherichia coli (E. coli) / References: UniProt: P47047, RNA helicase
#57: Protein/peptide MPP6 /


Mass: 954.168 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Production host: Escherichia coli (E. coli)

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Ribosome assembly ... , 2 types, 2 molecules Wx

#23: Protein/peptide Ribosome assembly factor MRT4 / mRNA turnover protein 4


Mass: 27098.012 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P33201
#47: Protein/peptide Ribosome assembly protein 4 / Notchless protein homolog 1 / Ribosome biogenesis factor RSA4


Mass: 57106.781 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P25382

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Nucleolar GTP-binding protein ... , 2 types, 2 molecules bm

#28: Protein/peptide Nucleolar GTP-binding protein 1


Mass: 74531.227 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q02892
#39: Protein/peptide Nucleolar GTP-binding protein 2


Mass: 55585.590 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P53742

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Ribosome biogenesis protein ... , 3 types, 3 molecules ruv

#42: Protein/peptide Ribosome biogenesis protein NSA2 / / NOP7-associated protein 2


Mass: 29786.783 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40078
#44: Protein/peptide Ribosome biogenesis protein RLP24 / / Ribosomal protein L24-like


Mass: 24027.650 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q07915
#45: Protein/peptide Ribosome biogenesis protein RPF2 /


Mass: 39665.789 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P36160

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Exosome complex ... , 2 types, 2 molecules KKLL

#54: Protein/peptide Exosome complex exonuclease RRP6 / Ribosomal RNA-processing protein 6


Mass: 84160.570 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RRP6, UNC733, YOR001W / Production host: Escherichia coli (E. coli)
References: UniProt: Q12149, Hydrolases, Acting on ester bonds, Exoribonucleases producing 5'-phosphomonoesters
#55: Protein/peptide Exosome complex protein LRP1 / / Like an rRNA processing protein 1 / Yeast C1D domain-containing protein / rRNA processing protein 47


Mass: 21086.297 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: LRP1, RRP47, YC1D, YHR081W / Production host: Escherichia coli (E. coli) / References: UniProt: P38801

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Non-polymers , 3 types, 8 molecules

#58: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Formula: Zn / Zinc
#59: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#60: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium

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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

Component
IDNameTypeEntity IDParent IDSource
1Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactorsCOMPLEX1, 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, 56, 570MULTIPLE SOURCES
2pre-60S particleRIBOSOME1, 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, 531NATURAL
3exosome nuclear cofactorsCOMPLEX54, 55, 56, 571RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
22559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
33559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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
Image recordingElectron dose: 38.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13rc2_2986: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 22439 / Symmetry type: POINT

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