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- PDB-5h4p: Structural snapshot of cytoplasmic pre-60S ribosomal particles bo... -

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Entry
Database: PDB / ID: 5h4p
TitleStructural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1
Descriptor60S ribosomal export protein NMD3
Eukaryotic translation initiation factor 6
Cytoplasmic 60S subunit biogenesis factor REH1/RNA Complex
(60S ribosomal protein ...) x 38
KeywordsRIBOSOME / pre-60S / Nmd3 / Lsg1 / assembly
Specimen sourceSaccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
MethodElectron microscopy (3.07 Å resolution / Particle / Single particle)
AuthorsMa, C. / Wu, S. / Li, N. / Chen, Y. / Yan, K. / Li, Z. / Zheng, L. / Lei, J. / Woolford, J.L. / Gao, N.
CitationNat. Struct. Mol. Biol., 2017, 24, 214-220

Nat. Struct. Mol. Biol., 2017, 24, 214-220 StrPapers
Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1.
Chengying Ma / Shan Wu / Ningning Li / Yan Chen / Kaige Yan / Zhifei Li / Lvqin Zheng / Jianlin Lei / John L Woolford / Ning Gao

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 1, 2016 / Release: Jan 25, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 25, 2017Structure modelrepositoryInitial release
1.1Mar 22, 2017Structure modelDatabase references
1.2Jun 14, 2017Structure modelOtherpdbx_database_status_pdbx_database_status.process_site

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Assembly

Deposited unit
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
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: 60S ribosomal protein L9-A
J: 60S ribosomal protein L11-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
W: 60S ribosomal protein L24-A
X: 60S ribosomal protein L25
Y: 60S ribosomal protein L26-A
Z: 60S ribosomal protein L27-A
a: 60S ribosomal protein L28
b: 60S ribosomal protein L29
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
o: 60S ribosomal protein L42-A
p: 60S ribosomal protein L43-A
w: 60S ribosomal export protein NMD3
y: Eukaryotic translation initiation factor 6
z: Cytoplasmic 60S subunit biogenesis factor REH1


Theoretical massNumber of molelcules
Total (without water)1,945,39544
Polyers1,945,39544
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)347240
ΔGint (kcal/M)-2789
Surface area (Å2)619010

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Components

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RNA chain , 3 types, 3 molecules 134

#1: RNA chain25S ribosomal RNA / 25S rRNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: 834774822
#2: RNA chain5S ribosomal RNA / 5S rRNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: 1039024045
#3: RNA chain5.8S ribosomal RNA / 5.8S rRNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: 1060743159

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60S ribosomal protein ... , 38 types, 38 molecules ABCDEFGHJL...

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


Mass: 26586.615 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX45

Cellular component

Molecular function

Biological process

#5: 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

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


Mass: 39027.926 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P10664

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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P26321

Cellular component

Molecular function

Biological process

#8: 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

#9: 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)
#10: 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

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


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

Cellular component

Molecular function

Biological process

#12: 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

#13: 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

#14: 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

#15: 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

#16: 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

#17: 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)
#18: 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

#19: 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

#20: 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

#21: 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

#22: 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

#23: 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

#24: Polypeptide(L)60S ribosomal protein L24-A / L30 / RP29 / YL21


Mass: 17661.717 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P04449

Cellular component

Molecular function

Biological process

#25: 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

#26: 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

#27: 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

#28: 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

#29: Polypeptide(L)60S ribosomal protein L29 / YL43


Mass: 6691.884 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05747

Cellular component

Molecular function

Biological process

#30: 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

#31: 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

#32: 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

#33: 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

#34: 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

#35: 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

#36: 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

#37: 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)
#38: Polypeptide(L)60S ribosomal protein L38


Mass: 8845.561 Da / Num. of mol.: 1
Details: MAREITDIKQFLELTRRADVKTATVKINKKLNKAGKPFRQTKFKVRGSSS LYTLVINDAG KAKKLIQSLPPTLKVNRL
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 (strain ATCC 204508 / S288c)
References: UniProt: P04650

Cellular component

Molecular function

Biological process

#40: Polypeptide(L)60S ribosomal protein L42-A / L41 / YL27 / YP44


Mass: 12246.658 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX27

Cellular component

Molecular function

Biological process

#41: 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) , 3 types, 3 molecules wyz

#42: Polypeptide(L)60S ribosomal export protein NMD3 / Nonsense-mediated mRNA decay protein 3


Mass: 27809.844 Da / Num. of mol.: 1 / Fragment: UNP residues 155-402
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P38861

Cellular component

Molecular function

Biological process

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


Mass: 24470.445 Da / Num. of mol.: 1 / Fragment: UNP residues 1-227
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)
#44: Polypeptide(L)Cytoplasmic 60S subunit biogenesis factor REH1 / REI1-homolog 1 / pre-60S factor REH1


Mass: 6737.835 Da / Num. of mol.: 1 / Fragment: UNP residues 377-432
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q06709

Cellular component

Molecular function

Biological process

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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: pre-60S-nmd3 complex / 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, 37, 38, 39, 40, 41, 42, 43, 44
Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 2 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 84240 / Symmetry type: POINT

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