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- PDB-5fl8: CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE -

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Basic information

Entry
Database: PDB / ID: 5fl8
TitleCRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE
KeywordsRIBOSOME
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: Oct 22, 2015 / Release: Dec 2, 2015
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 2, 2015Structure modelrepositoryInitial release
1.1Dec 9, 2015Structure modelDatabase references / Other
1.2Dec 23, 2015Structure modelOther
1.3Feb 3, 2016Structure modelDatabase references / Other / Source and taxonomy
1.4Apr 19, 2017Structure modelOther
1.5Aug 30, 2017Structure modelData collection / Derived calculationsem_software / struct_conn_em_software.image_processing_id

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Assembly

Deposited unit
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: Rpl9ap
I: 60S ribosomal protein L1-B
J: 60S ribosomal protein L11-A
K: 60S ribosomal protein L12-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
X: 60S ribosomal protein L25
Y: 60S ribosomal protein L26-A
Z: 60S ribosomal protein L27-A
a: 60S ribosomal protein L28
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: Eukaryotic translation initiation factor 6
n: Ribosome assembly factor MRT4
o: Nucleolar GTP-binding protein 1
p: 60S ribosomal protein L43-A
q: Ribosome assembly protein 4
r: Protein SDA1
s: Midasin
t: Ribosome biogenesis protein RLP24
u: ARX1
x: 25S ribosomal RNA
y: 5.8S ribosomal RNA
z: 5S ribosomal RNA


Theoretical massNumber of molelcules
Total (without water)2,592,65048
Polyers2,592,65048
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 ... , 36 types, 36 molecules ABCDEFGIJK...

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


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

Cellular component

Molecular function

Biological process

#2: 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 (strain ATCC 204508 / S288c)
References: UniProt: P14126

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

#4: 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 (strain ATCC 204508 / S288c)
References: UniProt: P26321

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


Mass: 27686.281 Da / Num. of mol.: 1
Source: (natural) 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)
#7: 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P17076

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)60S ribosomal protein L1-B / L10a


Mass: 24524.799 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX44

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


Mass: 20589.518 Da / Num. of mol.: 1
Source: (natural) 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)
#17: Polypeptide(L)60S ribosomal protein L18-A / RP28


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)60S ribosomal protein L35-A


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 7 types, 7 molecules Hmorstu

#8: Polypeptide(L)Rpl9ap


Mass: 21605.061 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: N1P1M8

Cellular component

Molecular function

Biological process

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


Mass: 26476.605 Da / Num. of mol.: 1
Source: (natural) 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)
#39: Polypeptide(L)Nucleolar GTP-binding protein 1


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

Cellular component

Molecular function

Biological process

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


Mass: 86755.578 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P53313

Cellular component

Biological process

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


Mass: 560352.875 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q12019

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)ARX1


Mass: 41870.898 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE

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

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


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

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)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)
References: UniProt: P25382

Cellular component

Biological process

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RNA chain , 3 types, 3 molecules xyz

#46: RNA chain25S ribosomal RNA


Mass: 898763.562 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE
#47: RNA chain5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE
#48: RNA chain5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: 834774822

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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 PARTICLE / Type: COMPLEX
Buffer solutionName: 50 MM TRIS, 100 MM NACL, 1.5 MM OR 5 MM MGCL2 / Details: 50 MM TRIS, 100 MM NACL, 1.5 MM OR 5 MM MGCL2 / pH: 7.5
SpecimenConc.: 2.06 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Jun 12, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 / Nominal defocus max: 4200 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC TVIPS
Image scansNumber digital images: 2659

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Processing

EM software
IDNameCategoryImage processing ID
1CootMODEL FITTING
2MDFFMODEL FITTING
3UCSF ChimeraMODEL FITTING
4SignaturePARTICLE SELECTION1
5SPIDERRECONSTRUCTION1
CTF correctionDetails: SUBVOLUMES
SymmetryPoint symmetry: C1
3D reconstructionResolution: 9.5 Å / Number of particles: 15749 / Nominal pixel size: 2.06 / Actual pixel size: 2.06
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3199
Symmetry type: POINT

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