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- PDB-5jcs: CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE -

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Entry
Database: PDB / ID: 5jcs
TitleCRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE
DescriptorEukaryotic translation initiation factor 6
Nucleolar GTP-binding protein 1
Protein SDA1
Midasin
Ribosome biogenesis protein RLP24
and more 3 items
KeywordsRIBOSOME / pre-60S ribosome rix1 rea1 / ribosome
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
MethodElectron microscopy (9.5 Å resolution / Particle / Single particle)
AuthorsBarrio-Garcia, C. / Thoms, M. / Flemming, D. / Kater, L. / Berninghausen, O. / Bassler, J. / Beckmann, R. / Hurt, E.
CitationNat. Struct. Mol. Biol., 2016, 23, 37-44

Nat. Struct. Mol. Biol., 2016, 23, 37-44 StrPapers
Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling.
Clara Barrio-Garcia / Matthias Thoms / Dirk Flemming / Lukas Kater / Otto Berninghausen / Jochen Baßler / Roland Beckmann / Ed Hurt

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 15, 2016 / Release: Nov 16, 2016
RevisionDateData content typeGroupProviderType
1.0Nov 16, 2016Structure modelrepositoryInitial release
1.1Dec 14, 2016Structure modelOther
1.2May 3, 2017Structure modelDatabase references

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Assembly

Deposited unit
A: 60S ribosomal protein L2-A
c: 60S ribosomal protein L30
B: 60S ribosomal protein L3
d: 60S ribosomal protein L31-A
C: 60S ribosomal protein L4-A
e: 60S ribosomal protein L32
D: 60S ribosomal protein L5
f: 60S ribosomal protein L33-A
E: 60S ribosomal protein L6-A
g: 60S ribosomal protein L34-A
F: 60S ribosomal protein L7-A
h: 60S ribosomal protein L35-A
G: 60S ribosomal protein L8-A
i: 60S ribosomal protein L36-A
H: 60S ribosomal protein L9-A
j: 60S ribosomal protein L37-A
I: 60S ribosomal protein L1-A
k: 60S ribosomal protein L38
J: 60S ribosomal protein L11-A
l: 60S ribosomal protein L39
K: 60S ribosomal protein L12-A
m: Eukaryotic translation initiation factor 6
L: 60S ribosomal protein L13-A
n: Ribosome assembly factor MRT4
M: 60S ribosomal protein L14-A
o: Nucleolar GTP-binding protein 1
N: 60S ribosomal protein L15-A
p: 60S ribosomal protein L43-A
O: 60S ribosomal protein L16-A
q: Ribosome assembly protein 4
P: 60S ribosomal protein L17-A
r: Protein SDA1
Q: 60S ribosomal protein L18-A
s: Midasin
R: 60S ribosomal protein L19-A
t: Ribosome biogenesis protein RLP24
S: 60S ribosomal protein L20-A
u: Probable metalloprotease ARX1
T: 60S ribosomal protein L21-A
x: 25S ribosomal RNA
U: 60S ribosomal protein L22-A
y: 5.8S ribosomal RNA
V: 60S ribosomal protein L23-A
z: 5S ribosomal RNA
X: 60S ribosomal protein L25
Y: 60S ribosomal protein L26-A
Z: 60S ribosomal protein L27-A
a: 60S ribosomal protein L28


Theoretical massNumber of molelcules
Total (without water)2,814,39848
Polyers2,814,39848
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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60S ribosomal protein ... , 37 types, 37 molecules AcBdCeDfEg...

#1: Polypeptide(L)60S ribosomal protein L2-A / L5 / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX45

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)60S ribosomal protein L30 / L32 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P14120

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)60S ribosomal protein L3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P14126

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)60S ribosomal protein L31-A / L34 / YL28


Mass: 12980.158 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0C2H8

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)60S ribosomal protein L4-A / L2 / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P10664

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)60S ribosomal protein L32


Mass: 14809.441 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P38061

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)60S ribosomal protein L5 / L1 / L1a / Ribosomal 5S RNA-binding protein / YL3


Mass: 33764.828 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P26321

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)60S ribosomal protein L33-A / L37 / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05744

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)60S ribosomal protein L6-A / L17 / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q02326

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)60S ribosomal protein L34-A


Mass: 13673.196 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P87262

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)60S ribosomal protein L7-A / L6 / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05737

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of LSU-rRNA (GO: 0000470)
  • maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000463)
  • ribosomal large subunit biogenesis (GO: 0042273)
#12: Polypeptide(L)60S ribosomal protein L35-A


Mass: 13942.640 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX84

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P17076

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)60S ribosomal protein L36-A / L39 / YL39


Mass: 11151.259 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05745

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)60S ribosomal protein L9-A / L8 / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05738

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)60S ribosomal protein L37-A / L43 / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P49166

Cellular component

Molecular function

Biological process

  • cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000448)
  • cytoplasmic translation (GO: 0002181)
  • translation (GO: 0006412)
#17: Polypeptide(L)60S ribosomal protein L1-A / L10a


Mass: 24524.799 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX43

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)60S ribosomal protein L38


Mass: 8845.561 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P49167

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)60S ribosomal protein L11-A / L16 / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0C0W9

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)60S ribosomal protein L39 / L46 / YL40


Mass: 6358.640 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P04650

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)60S ribosomal protein L12-A / L15 / YL23


Mass: 17850.621 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX53

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)60S ribosomal protein L13-A


Mass: 22604.164 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q12690

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)60S ribosomal protein L14-A


Mass: 15195.066 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P36105

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)60S ribosomal protein L15-A / L13 / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05748

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)60S ribosomal protein L43-A / L37a / YL35


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

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)60S ribosomal protein L16-A / L13a / L21 / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P26784

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)60S ribosomal protein L17-A / L20A / YL17


Mass: 20589.518 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05740

Cellular component

Molecular function

Biological process

  • cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000448)
  • cytoplasmic translation (GO: 0002181)
#33: Polypeptide(L)60S ribosomal protein L18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX49

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)60S ribosomal protein L19-A / L23 / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX82

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)60S ribosomal protein L20-A / L18a


Mass: 20478.852 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX23

Cellular component

Molecular function

Biological process

#39: Polypeptide(L)60S ribosomal protein L21-A


Mass: 18279.266 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q02753

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)60S ribosomal protein L22-A / L1c / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05749

Cellular component

Molecular function

Biological process

#43: Polypeptide(L)60S ribosomal protein L23-A / L17a / YL32


Mass: 14493.950 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX41

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)60S ribosomal protein L25 / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P04456

Cellular component

Molecular function

Biological process

#46: Polypeptide(L)60S ribosomal protein L26-A / L33 / YL33


Mass: 14265.784 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05743

Cellular component

Molecular function

Biological process

#47: Polypeptide(L)60S ribosomal protein L27-A


Mass: 15568.360 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0C2H6

Cellular component

Molecular function

Biological process

#48: Polypeptide(L)60S ribosomal protein L28 / L27a / L29 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P02406

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 6 types, 6 molecules morstu

#22: Polypeptide(L)Eukaryotic translation initiation factor 6 / eIF-6


Mass: 26476.605 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q12522

Cellular component

Molecular function

Biological process

  • assembly of large subunit precursor of preribosome (GO: 1902626)
  • maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000466)
  • maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000463)
  • mature ribosome assembly (GO: 0042256)
  • ribosomal large subunit biogenesis (GO: 0042273)
  • ribosomal subunit export from nucleus (GO: 0000054)
  • rRNA processing (GO: 0006364)
#26: Polypeptide(L)Nucleolar GTP-binding protein 1


Mass: 74531.227 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q02892

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)Protein SDA1 / Severe depolymerization of actin protein 1


Mass: 86755.578 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae / References: UniProt: P53313

Cellular component

Biological process

#34: Polypeptide(L)Midasin / MIDAS-containing protein / Ribosome export/assembly protein 1


Mass: 559951.438 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q12019

Cellular component

Molecular function

Biological process

#36: Polypeptide(L)Ribosome biogenesis protein RLP24 / Ribosomal protein L24-like


Mass: 24027.650 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q07915

Cellular component

Molecular function

Biological process

#38: Polypeptide(L)Probable metalloprotease ARX1 / Associated with ribosomal export complex protein 1


Mass: 65290.336 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q03862, EC: 3.-.-.-

Cellular component

Molecular function

Biological process

  • ribosomal large subunit export from nucleus (GO: 0000055)

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Ribosome assembly ... , 2 types, 2 molecules nq

#24: Polypeptide(L)Ribosome assembly factor MRT4 / mRNA turnover protein 4


Mass: 27098.012 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P33201

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)Ribosome assembly protein 4 / Notchless protein homolog 1 / Ribosome biogenesis factor RSA4


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

Cellular component

Biological process

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RNA chain , 3 types, 3 molecules xyz

#40: RNA chain25S ribosomal RNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae / References: GenBank: 834774822
#42: RNA chain5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae / References: GenBank: 1036126960
#44: RNA chain5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae / References: GenBank: 1039022925

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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: Rix1-Rea1 pre-60S particle / 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
Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae
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: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 9.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 15749 / Symmetry type: POINT

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