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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
DescriptorWD40 domain proteins, UTP10, UTP-A oligomerization domain, UTP21, UTP6, UTP-B oligomerisation domain, Pre mRNA splicing protein, Snu13, Nop1, rrp9, Rcl1, Bms1, Imp3, Imp4, Utp24, Emg1, KRR1 small subunit processome component, Kre33, Utp30, eS1, eS4, uS7, eS6, eS7, eS8, uS4, uS15, uS11, uS9, uS17, uS8, eS24, eS28/RNA Complex
KeywordsRIBOSOME / nuclear RNP / Ribosome
Specimen sourceChaetomium thermophilum / fungus
Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
MethodElectron microscopy (7.3 Å resolution / Particle / Single particle)
AuthorsTurk, M. / Cheng, J. / Berninghausen, O. / Kornprobst, M. / Flemming, D. / Kos-Braun, I.C. / Kos, M. / Thoms, M. / Hurt, E. / Beckmann, R.
CitationCell, 2016, 166, 380-393

Cell, 2016, 166, 380-393 StrPapers
Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome.
Markus Kornprobst / Martin Turk / Nikola Kellner / Jingdong Cheng / Dirk Flemming / Isabelle Koš-Braun / Martin Koš / Matthias Thoms / Otto Berninghausen / Roland Beckmann / Ed Hurt

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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WD40 domain ... , 2 types, 16 molecules ABCDEFJKLN...

#1: Polypeptide(L)
WD40 domain proteins


Mass: 109801.734 Da / Num. of mol.: 13 / Source: (natural) Chaetomium thermophilum
#5: Polypeptide(L)WD40 domain proteins


Mass: 74058.758 Da / Num. of mol.: 3 / Source: (natural) Chaetomium thermophilum

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Polypeptide(L) , 32 types, 38 molecules GHIQRSTUVW...

#2: Polypeptide(L)UTP10


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


Mass: 78313.859 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum
#4: Polypeptide(L)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)
References: UniProt: Q06078

Cellular component

Biological process

#6: Polypeptide(L)UTP6


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


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


Mass: 46765.828 Da / Num. of mol.: 2 / Source: (natural) Chaetomium thermophilum

Molecular function

Biological process

#9: Polypeptide(L)Snu13


Mass: 14074.316 Da / Num. of mol.: 2 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)Nop1


Mass: 26455.375 Da / Num. of mol.: 2 / Source: (natural) Chaetomium thermophilum

Molecular function

Biological process

#11: Polypeptide(L)rrp9


Mass: 65146.969 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)Rcl1


Mass: 40220.559 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

  • endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000480)
  • 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) (GO: 0000447)
  • endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000472)
  • rRNA methylation (GO: 0031167)
  • rRNA processing (GO: 0006364)
#13: Polypeptide(L)Bms1


Mass: 135792.281 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

  • endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000480)
  • endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000472)
  • rRNA methylation (GO: 0031167)
#14: Polypeptide(L)Imp3


Mass: 21802.396 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum / References: UniProt: G0SDL4

Cellular component

Molecular function

#15: Polypeptide(L)Putative U3 small nucleolar ribonucleoprotein


Mass: 34216.266 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum / References: UniProt: G0SE90

Cellular component

#16: Polypeptide(L)Utp24


Mass: 21103.770 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum / References: UniProt: G0SE30

Cellular component

#17: Polypeptide(L)Emg1


Mass: 27936.461 Da / Num. of mol.: 2 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

  • endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000480)
  • 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) (GO: 0000447)
  • endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000472)
  • ribosomal small subunit biogenesis (GO: 0042274)
  • rRNA base methylation (GO: 0070475)
  • rRNA methylation (GO: 0031167)
  • rRNA processing (GO: 0006364)
#18: Polypeptide(L)KRR1 small subunit processome component / KRR-R motif-containing protein 1


Mass: 37500.777 Da / Num. of mol.: 2 / Source: (natural) Chaetomium thermophilum / References: UniProt: G0S3V7

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)Kre33


Mass: 119795.125 Da / Num. of mol.: 2 / Source: (natural) Chaetomium thermophilum / References: UniProt: G0S273

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)Utp30


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


Mass: 29709.248 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)eS4


Mass: 29512.164 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)uS7


Mass: 25072.600 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)eS6


Mass: 32614.617 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)eS7


Mass: 23231.061 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)eS8


Mass: 24250.346 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)
#27: Polypeptide(L)uS4


Mass: 22487.893 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • positive regulation of translational fidelity (GO: 0045903)
  • rRNA methylation (GO: 0031167)
#28: Polypeptide(L)uS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)uS11


Mass: 14562.655 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)uS9


Mass: 15877.490 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)uS17


Mass: 18142.395 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)uS8


Mass: 14650.062 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)eS24


Mass: 17128.072 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)
#34: Polypeptide(L)eS28


Mass: 7605.847 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum

Cellular component

Molecular function

Biological process

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RNA chain , 2 types, 2 molecules 23

#35: RNA chain18S ribosomal RNA


Mass: 579761.938 Da / Num. of mol.: 1 / Source: (natural) Chaetomium thermophilum
#36: RNA chainU3 RNA


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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
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 FIELD
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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