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- PDB-5jpq: Cryo-EM structure of the 90S pre-ribosome -

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Entry
Database: PDB / ID: 5jpq
TitleCryo-EM structure of the 90S pre-ribosome
Components
  • (WD40 domain proteins) x 2
  • 18S ribosomal RNA
  • Bms1
  • Emg1
  • Imp3
  • KRR1 small subunit processome component
  • Kre33
  • Nop1
  • Pre mRNA splicing protein
  • Putative U3 small nucleolar ribonucleoprotein
  • Rcl1
  • Snu13
  • U3 RNA
  • U3 small nucleolar RNA-associated protein 21
  • UTP-A oligomerization domain
  • UTP-B oligomerisation domain
  • UTP10
  • UTP6
  • Utp24
  • Utp30
  • eS1
  • eS24
  • eS28
  • eS4
  • eS6
  • eS7
  • eS8
  • rrp9
  • uS11
  • uS15
  • uS17
  • uS4
  • uS7
  • uS8
  • uS9
KeywordsRIBOSOME / nuclear RNP / Ribosome
Function / homologyRNA 3'-terminal phosphate cyclase domain / tRNA (guanine-N1-)-methyltransferase, N-terminal / Ribosomal protein S7 domain / Ribosomal RNA assembly KRR1 / Anaphase-promoting complex subunit 4, WD40 domain / P-loop containing nucleoside triphosphate hydrolase / 40S ribosomal protein S1/3, eukaryotes / Possible tRNA binding domain / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein ...RNA 3'-terminal phosphate cyclase domain / tRNA (guanine-N1-)-methyltransferase, N-terminal / Ribosomal protein S7 domain / Ribosomal RNA assembly KRR1 / Anaphase-promoting complex subunit 4, WD40 domain / P-loop containing nucleoside triphosphate hydrolase / 40S ribosomal protein S1/3, eukaryotes / Possible tRNA binding domain / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / Helix hairpin bin domain superfamily / Alpha/beta knot methyltransferases / Ribosomal protein S15P / PIN-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10 / Ribosomal protein S8 superfamily / Nop domain superfamily / Ribosomal protein L1-like / Ribosomal protein S4/S9 / RNA 3'-terminal phosphate cyclase, insert domain superfamily / Ribosomal protein S3Ae, conserved site / Ribosomal protein L2, domain 2 / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / Ribosomal protein L1, 3-layer alpha/beta-sandwich / RNA 3'-terminal phosphate cyclase type 2 / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein L7Ae, archaea / Ribosomal protein L7Ae/L8/Nhp2 family / WD40 repeat, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / RNA 3'-terminal phosphate cyclase-like, conserved site / Fibrillarin, conserved site / U3 small nucleolar RNA-associated protein 10 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / WD40-repeat-containing domain superfamily / K Homology domain, type 1 superfamily / Ribosomal protein S9 signature. / AARP2CN (NUC121) domain / snoRNA binding domain, fibrillarin / EMG1/NEP1 methyltransferase / Utp21 specific WD40 associated putative domain / Brix domain / Fcf1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / Helicase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / BP28CT (NUC211) domain / Ribosomal protein S24e / Domain of unknown function (DUF1726) / U3 small nucleolar RNA-associated protein 10 / Anaphase-promoting complex subunit 4 WD40 domain / GNAT acetyltransferase 2 / Possible tRNA binding domain / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / S4 domain / Fibrillarin / Ribosomal protein S7 domain superfamily / Ribosomal protein S17 / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / rRNA-processing protein Fcf1, PIN domain / Ribosome biogenesis protein Bms1, N-terminal / Ribosomal protein S4e, central domain superfamily / ATPase family associated with various cellular activities (AAA) / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S15 / Ribosomal protein S9/S16 / Ribosomal protein S7e / WD domain, G-beta repeat / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein L1p/L10e family / Ribosomal family S4e / Ribosomal S3Ae family / Ribosomal protein S6e / RNA 3'-terminal phosphate cyclase
Function and homology information
Specimen sourceChaetomium thermophilum (fungus)
Saccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 7.3 Å resolution
AuthorsTurk, M. / Cheng, J. / Berninghausen, O. / Kornprobst, M. / Flemming, D. / Kos-Braun, I.C. / Kos, M. / Thoms, M. / Hurt, E. / Beckmann, R.
CitationJournal: Cell / Year: 2016
Title: Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome.
Authors: Markus Kornprobst / Martin Turk / Nikola Kellner / Jingdong Cheng / Dirk Flemming / Isabelle Koš-Braun / Martin Koš / Matthias Thoms / Otto Berninghausen / Roland Beckmann / Ed Hurt
Abstract: The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that ...The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that associate with nascent pre-rRNA. We report the cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome, revealing how a network of biogenesis factors including 19 β-propellers and large α-solenoid proteins engulfs the pre-rRNA. Within the 90S pre-ribosome, we identify the UTP-A, UTP-B, Mpp10-Imp3-Imp4, Bms1-Rcl1, and U3 snoRNP modules, which are organized around 5'-ETS and partially folded 18S rRNA. The U3 snoRNP is strategically positioned at the center of the 90S particle to perform its multiple tasks during pre-rRNA folding and processing. The architecture of the elusive 90S pre-ribosome gives unprecedented structural insight into the early steps of pre-rRNA maturation. Nascent rRNA that is co-transcriptionally folded and given a particular shape by encapsulation within a dedicated mold-like structure is reminiscent of how polypeptides use chaperone chambers for their protein folding.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 4, 2016 / Release: Jul 27, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 27, 2016Structure modelrepositoryInitial release
1.1Aug 3, 2016Structure modelOther
1.2Jul 5, 2017Structure modelStructure summaryentity_entity.pdbx_description

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Assembly

Deposited unit
A: WD40 domain proteins
B: WD40 domain proteins
C: WD40 domain proteins
D: WD40 domain proteins
E: WD40 domain proteins
F: WD40 domain proteins
G: UTP10
H: UTP-A oligomerization domain
I: U3 small nucleolar RNA-associated protein 21
J: WD40 domain proteins
K: WD40 domain proteins
L: WD40 domain proteins
M: WD40 domain proteins
N: WD40 domain proteins
O: WD40 domain proteins
P: WD40 domain proteins
Q: UTP6
R: UTP-B oligomerisation domain
S: Pre mRNA splicing protein
T: Pre mRNA splicing protein
U: Snu13
V: Snu13
W: Nop1
X: Nop1
Y: rrp9
Z: Rcl1
a: Bms1
b: Imp3
c: Putative U3 small nucleolar ribonucleoprotein
d: Utp24
e: Emg1
f: Emg1
g: KRR1 small subunit processome component
h: KRR1 small subunit processome component
i: Kre33
j: Kre33
k: Utp30
l: WD40 domain proteins
m: WD40 domain proteins
n: WD40 domain proteins
o: eS1
p: eS4
q: uS7
r: eS6
s: eS7
t: eS8
u: uS4
v: uS15
w: uS11
x: uS9
y: uS17
z: uS8
0: eS24
1: eS28
2: 18S ribosomal RNA
3: U3 RNA


Theoretical massNumber of molelcules
Total (without water)3,984,52656
Polyers3,984,52656
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 34 types, 54 molecules ABCDEFJKLNPlnGHIMOmQRSTUVWXYZa...

#1: Protein/peptide
WD40 domain proteins


Mass: 109801.734 Da / Num. of mol.: 13 / Source: (natural) Chaetomium thermophilum (fungus)
#2: Protein/peptide UTP10


Mass: 198508.438 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S5L1
#3: Protein/peptide UTP-A oligomerization domain


Mass: 78313.859 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus)
#4: 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)
References: UniProt: Q06078
#5: Protein/peptide WD40 domain proteins


Mass: 74058.758 Da / Num. of mol.: 3 / Source: (natural) Chaetomium thermophilum (fungus)
#6: Protein/peptide UTP6 /


Mass: 38825.836 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus)
#7: Protein/peptide UTP-B oligomerisation domain


Mass: 47676.848 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus)
#8: Protein/peptide Pre mRNA splicing protein


Mass: 46765.828 Da / Num. of mol.: 2 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: A0A0E3MJI1*PLUS
#9: Protein/peptide Snu13


Mass: 14074.316 Da / Num. of mol.: 2 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P55858*PLUS
#10: Protein/peptide Nop1


Mass: 26455.375 Da / Num. of mol.: 2 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P58032*PLUS
#11: Protein/peptide rrp9 /


Mass: 65146.969 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q06506*PLUS
#12: Protein/peptide Rcl1 /


Mass: 40220.559 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q08096*PLUS
#13: Protein/peptide Bms1


Mass: 135792.281 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q08965*PLUS
#14: Protein/peptide Imp3 /


Mass: 21802.396 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SDL4
#15: Protein/peptide Putative U3 small nucleolar ribonucleoprotein


Mass: 34216.266 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum / References: UniProt: G0SE90
#16: Protein/peptide Utp24


Mass: 21103.770 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SE30
#17: Protein/peptide Emg1 /


Mass: 27936.461 Da / Num. of mol.: 2 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q06287*PLUS
#18: Protein/peptide KRR1 small subunit processome component / / KRR-R motif-containing protein 1


Mass: 37500.777 Da / Num. of mol.: 2 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S3V7
#19: Protein/peptide Kre33


Mass: 119795.125 Da / Num. of mol.: 2 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S273
#20: Protein/peptide Utp30


Mass: 43700.527 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S7X0
#21: Protein/peptide eS1


Mass: 29709.248 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q23DE3*PLUS
#22: Protein/peptide eS4


Mass: 29512.164 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P0C233*PLUS
#23: Protein/peptide uS7


Mass: 25072.600 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P26783*PLUS
#24: Protein/peptide eS6


Mass: 32614.617 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: A4VD76*PLUS
#25: Protein/peptide eS7


Mass: 23231.061 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: I7MD19*PLUS
#26: Protein/peptide eS8


Mass: 24250.346 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q22AV0*PLUS
#27: Protein/peptide uS4


Mass: 22487.893 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: O13516*PLUS
#28: Protein/peptide uS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P05756*PLUS
#29: Protein/peptide uS11


Mass: 14562.655 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P06367*PLUS
#30: Protein/peptide uS9


Mass: 15877.490 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P0CX51*PLUS
#31: Protein/peptide uS17


Mass: 18142.395 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q22B78*PLUS
#32: Protein/peptide uS8


Mass: 14650.062 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P0C0W1*PLUS
#33: Protein/peptide eS24


Mass: 17128.072 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: I7MAL3*PLUS
#34: Protein/peptide eS28


Mass: 7605.847 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q3E7X9*PLUS

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RNA chain , 2 types, 2 molecules 23

#35: RNA chain 18S ribosomal RNA /


Mass: 579761.938 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus)
#36: RNA chain U3 RNA


Mass: 87969.609 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum (fungus)

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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 pre-ribosome / Type: RIBOSOME
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
Source: NATURAL
Source (natural)Organism: Chaetomium thermophilum (fungus)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 16 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 43000 / Symmetry type: POINT

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