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- PDB-4v7f: Arx1 pre-60S particle. -

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Entry
Database: PDB / ID: 4v7f
TitleArx1 pre-60S particle.
DescriptorArx1 pre-60S particle.
KeywordsRIBOSOME / 60S biogenesis / 5S rRNA
Specimen sourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
MethodElectron microscopy (8.7 Å resolution / Particle / Single particle)
AuthorsLeidig, C. / Thoms, M. / Holdermann, I. / Bradatsch, B. / Berninghausen, O. / Bange, G. / Sinning, I. / Hurt, E. / Beckmann, R.
CitationNat Commun, 2014, 5, 3491-3491

Nat Commun, 2014, 5, 3491-3491 Yorodumi Papers
60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle.
Christoph Leidig / Matthias Thoms / Iris Holdermann / Bettina Bradatsch / Otto Berninghausen / Gert Bange / Irmgard Sinning / Ed Hurt / Roland Beckmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 10, 2013 / Release: Jul 9, 2014
RevisionDateData content typeGroupProviderType
1.0Jul 9, 2014Structure modelrepositoryInitial release
1.1Dec 10, 2014Structure modelOther
1.2Apr 15, 2015Structure modelOther

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Assembly

Deposited unit
1: 25S ribosomal RNA
2: 5.8S ribosomal RNA
3: 5S ribosomal RNA
A: 60S ribosomal protein L1
B: 60S ribosomal protein L2
C: 60S ribosomal protein L3
D: 60S ribosomal protein L4
E: 60S ribosomal protein L11
F: 60S ribosomal protein L9
G: 60S ribosomal protein L6
H: 60S ribosomal protein L8
I: 60S ribosomal protein L12
J: 60S ribosomal protein L16
K: 60S ribosomal protein L13
L: 60S ribosomal protein L23
M: 60S ribosomal protein L14
N: 60S ribosomal protein L28
O: 60S ribosomal protein L15
P: 60S ribosomal protein L5
Q: 60S ribosomal protein L18
R: 60S ribosomal protein L19
S: 60S ribosomal protein L20
T: 60S ribosomal protein L21
U: 60S ribosomal protein L17
V: 60S ribosomal protein L22
W: 60S ribosomal protein L25
X: 60S ribosomal protein L26
Y: 60S ribosomal protein L27
Z: 60S ribosomal protein L35
a: 60S ribosomal protein L7
b: 60S ribosomal protein L30
c: 60S ribosomal protein L31
d: 60S ribosomal protein L32
e: 60S ribosomal protein L33
f: 60S ribosomal protein L34
g: 60S ribosomal protein L36
h: 60S ribosomal protein L37
i: 60S ribosomal protein L38
j: 60S ribosomal protein L39
k: 60S ribosomal protein L43
l: metalloprotease ARX1
m: Eukaryotic translation initiation factor 6
n: mRNA turnover protein 4
o: Nucleolar GTP-binding protein 1
p: Ribosome biogenesis protein RLP24
q: Ribosome assembly protein 4
r: Ribosome biogenesis protein RLP7
s: Ribosome biogenesis protein RLP7


Theoretical massNumber of molelcules
Total (without water)2,240,93348
Polyers2,240,93348
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 3 types, 3 molecules 123

#1: RNA chain25S ribosomal RNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae
#2: RNA chain5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae
#3: RNA chain5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae

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60S ribosomal protein ... , 37 types, 37 molecules ABCDEFGHIJ...

#4: Polypeptide(L)60S ribosomal protein L1 / L10a


Mass: 24524.799 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX43

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)60S ribosomal protein L2 / L5 / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX45

Cellular component

Molecular function

Biological process

#6: 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: (natural) Saccharomyces cerevisiae / References: UniProt: P14126

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)60S ribosomal protein L4 / L2 / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P10664

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)60S ribosomal protein L11 / L16 / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0C0W9

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)60S ribosomal protein L9 / L8 / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05738

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)60S ribosomal protein L6 / L17 / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q02326

Cellular component

Molecular function

Biological process

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


Mass: 28175.820 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P17076

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)60S ribosomal protein L12 / L15 / YL23


Mass: 17850.621 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX53

Cellular component

Molecular function

Biological process

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


Mass: 22247.227 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P26784

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)60S ribosomal protein L13


Mass: 22604.164 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q12690

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)60S ribosomal protein L23 / L17a / YL32


Mass: 14493.950 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX41

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)60S ribosomal protein L14


Mass: 15195.066 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P36105

Cellular component

Molecular function

Biological process

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


Mass: 16761.666 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P02406

Cellular component

Molecular function

Biological process

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


Mass: 24482.357 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05748

Cellular component

Molecular function

Biological process

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


Mass: 33764.828 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P26321

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)60S ribosomal protein L18 / RP28


Mass: 20609.252 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX49

Cellular component

Molecular function

Biological process

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


Mass: 21762.316 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX82

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)60S ribosomal protein L20 / L18a


Mass: 20478.852 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX23

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)60S ribosomal protein L21


Mass: 18279.266 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q02753

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)60S ribosomal protein L17 / L20A / YL17


Mass: 20589.518 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / 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)
#25: Polypeptide(L)60S ribosomal protein L22 / L1c / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05749

Cellular component

Molecular function

Biological process

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


Mass: 15787.612 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P04456

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)60S ribosomal protein L26 / L33 / YL33


Mass: 14265.784 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05743

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)60S ribosomal protein L27


Mass: 15568.360 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0C2H6

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)60S ribosomal protein L35


Mass: 13942.640 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX84

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)60S ribosomal protein L7 / L6 / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / 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)
#31: Polypeptide(L)60S ribosomal protein L30 / L32 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P14120

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)60S ribosomal protein L31 / L34 / YL28


Mass: 12980.158 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0C2H8

Cellular component

Molecular function

Biological process

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


Mass: 14809.441 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P38061

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)60S ribosomal protein L33 / L37 / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05744

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)60S ribosomal protein L34


Mass: 13673.196 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P87262

Cellular component

Molecular function

Biological process

#36: Polypeptide(L)60S ribosomal protein L36 / L39 / YL39


Mass: 11151.259 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05745

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)60S ribosomal protein L37 / L43 / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / 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)
#38: Polypeptide(L)60S ribosomal protein L38


Mass: 8845.561 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P49167

Cellular component

Molecular function

Biological process

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


Mass: 6358.640 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P04650

Cellular component

Molecular function

Biological process

#40: Polypeptide(L)60S ribosomal protein L43 / L37a / YL35


Mass: 10112.952 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX25

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 5 types, 5 molecules lmnoq

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


Mass: 65290.336 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q03862, EC: 3.-.-.-

Cellular component

Molecular function

Biological process

  • ribosomal large subunit export from nucleus (GO: 0000055)
#42: Polypeptide(L)Eukaryotic translation initiation factor 6 / Tif6 / eIF-6


Mass: 26476.605 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / 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)
#43: Polypeptide(L)mRNA turnover protein 4 / Mrt4


Mass: 27098.012 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P33201

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)Nucleolar GTP-binding protein 1 / Nog1


Mass: 74531.227 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q02892

Cellular component

Molecular function

Biological process

#46: Polypeptide(L)Ribosome assembly protein 4 / Rsa4


Mass: 57106.781 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P25382

Cellular component

Biological process

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Ribosome biogenesis protein ... , 2 types, 3 molecules prs

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


Mass: 24027.650 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q07915

Cellular component

Molecular function

Biological process

#47: Polypeptide(L)Ribosome biogenesis protein RLP7 / Ribosomal protein L7-like


Mass: 36621.074 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P40693

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000465)
  • maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000463)
  • ribosomal large subunit biogenesis (GO: 0042273)

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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

Component
IDNameTypeParent ID
1Arx1 pre-60S particleRIBOSOME0
2Arx1 pre-60S particleRIBOSOME1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Nov 12, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SymmetryPoint symmetry: C1
3D reconstructionResolution: 8.7 Å / Number of particles: 75887 / Nominal pixel size: 1.0605 / Actual pixel size: 1.0605 / Symmetry type: POINT
Atomic model buildingPDB-ID: 3U5D
Number of atoms included #LASTProtein: 0 / Nucleic acid: 22036 / Ligand: 0 / Solvent: 0 / Total: 22036

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