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- PDB-5gak: Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A -

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Basic information

Entry
Database: PDB / ID: 5gak
TitleYeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A
DescriptorUbiquitin-60S ribosomal protein L40
Eukaryotic translation initiation factor 5A-1
L1-A
(60S ribosomal protein ...) x 40
KeywordsRIBOSOME / ribosome / translation / hypusine
Specimen sourceSaccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
MethodElectron microscopy (3.88 Å resolution / Particle / Single particle)
AuthorsSchmidt, C. / Becker, T.
CitationNucleic Acids Res., 2016, 44, 1944-1951

Nucleic Acids Res., 2016, 44, 1944-1951 StrPapers
Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome.
Christian Schmidt / Thomas Becker / André Heuer / Katharina Braunger / Vivekanandan Shanmuganathan / Markus Pech / Otto Berninghausen / Daniel N Wilson / Roland Beckmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 9, 2015 / Release: Feb 24, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 24, 2016Structure modelrepositoryInitial release
1.1Mar 16, 2016Structure modelDatabase references
1.2Aug 2, 2017Structure modelData collection / Derived calculationsem_image_scans / em_software / struct_conn_em_software.name

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Assembly

Deposited unit
1: 25S rRNA
X: 60S ribosomal protein L23-A
3: 5S rRNA
Y: 60S ribosomal protein L24-A
4: 5.8S rRNA
Z: 60S ribosomal protein L25
A: The A-site tRNA was modeled based on an E. coli tRNA-Lys
a: 60S ribosomal protein L26-A
B: P-site tRNA
b: 60S ribosomal protein L27-A
C: 60S ribosomal protein L42-A
c: 60S ribosomal protein L28
D: 60S ribosomal protein L43-A
d: 60S ribosomal protein L29
E: 60S ribosomal protein L2-A
e: 60S ribosomal protein L30
F: 60S ribosomal protein L3
f: 60S ribosomal protein L31-A
G: 60S ribosomal protein L4-A
g: 60S ribosomal protein L32
H: 60S ribosomal protein L5
h: 60S ribosomal protein L33-A
I: 60S ribosomal protein L6-A
i: 60S ribosomal protein L34-A
J: 60S ribosomal protein L7-A
j: 60S ribosomal protein L35-A
K: 60S ribosomal protein L8-A
k: 60S ribosomal protein L36-A
L: 60S ribosomal protein L9-A
l: 60S ribosomal protein L37-A
M: 60S ribosomal protein L11-A
m: 60S ribosomal protein L38
N: 60S ribosomal protein L13-A
n: 60S ribosomal protein L39
O: 60S ribosomal protein L14-B
o: Ubiquitin-60S ribosomal protein L40
P: 60S ribosomal protein L15-A
p: 60S ribosomal protein L41-A
Q: 60S ribosomal protein L16-A
q: Eukaryotic translation initiation factor 5A-1
R: 60S ribosomal protein L17-A
r: ribosomal protein RPL1
S: 60S ribosomal protein L18-A
s: 60S ribosomal protein L10
T: 60S ribosomal protein L19-A
U: 60S ribosomal protein L20-A
V: 60S ribosomal protein L21-A
W: 60S ribosomal protein L22-A
z: nascent polypeptide chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,016,96650
Polyers2,016,68549
Non-polymers2811
Water0
#1


  • idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)363990
ΔGint (kcal/M)-2886
Surface area (Å2)668230
MethodPISA

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Components

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RNA chain , 5 types, 5 molecules 134AB

#1: RNA chain25S rRNA


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


Mass: 38951.105 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: 834774822
#5: RNA chain5.8S rRNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: 940534893
#7: RNA chainThe A-site tRNA was modeled based on an E. coli tRNA-Lys


Mass: 24378.408 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae
#9: RNA chainP-site tRNA


Mass: 24815.684 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae

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60S ribosomal protein ... , 40 types, 40 molecules XYZabCcDdE...

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

#6: 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

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

#12: 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

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

#16: 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

#17: 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

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


Mass: 12649.754 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0C2H8

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

#20: 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

#21: 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

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)60S ribosomal protein L7-A / 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)
#26: Polypeptide(L)60S ribosomal protein L35-A


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

Cellular component

Molecular function

Biological process

#27: 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 / References: UniProt: P17076

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)60S ribosomal protein L37-A / 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)
#31: Polypeptide(L)60S ribosomal protein L11-A / L16 / RP39 / YL22


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

Cellular component

Molecular function

Biological process

#32: 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

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


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

Cellular component

Molecular function

Biological process

#34: 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

#35: Polypeptide(L)60S ribosomal protein L14-B


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

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)60S ribosomal protein L15-A / 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

#38: Polypeptide(L)60S ribosomal protein L41-A / L47 / YL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX86

Cellular component

Molecular function

Biological process

#39: Polypeptide(L)60S ribosomal protein L16-A / 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

#41: Polypeptide(L)60S ribosomal protein L17-A / 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)
#43: Polypeptide(L)60S ribosomal protein L18-A / RP28


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

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)60S ribosomal protein L10 / L9 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25410.465 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P41805

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)60S ribosomal protein L19-A / 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

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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


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

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 4 types, 4 molecules oqrz

#36: Polypeptide(L)Ubiquitin-60S ribosomal protein L40


Mass: 14583.077 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CH08

Cellular component

Molecular function

Biological process

#40: Polypeptide(L)Eukaryotic translation initiation factor 5A-1 / eIF-5A-1 / Hypusine-containing protein HP2 / eIF-4D


Mass: 17222.406 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P23301

Cellular component

Molecular function

Biological process

  • positive regulation of cytoplasmic translational elongation through polyproline stretches (GO: 1903272)
  • positive regulation of translational elongation (GO: 0045901)
  • positive regulation of translational initiation (GO: 0045948)
  • positive regulation of translational termination (GO: 0045905)
  • translational frameshifting (GO: 0006452)
#42: Polypeptide(L)ribosomal protein RPL1


Mass: 17889.996 Da / Num. of mol.: 1
Details: The sequence of yeast RPL1 corresponds to UniProt (P26321)
Source: (natural) Saccharomyces cerevisiae
#49: Polypeptide(L)nascent polypeptide chain


Mass: 1975.426 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae

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Non-polymers , 1 types, 1 molecules

#50: ChemicalChemComp-3HE / 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione


Mass: 281.347 Da / Num. of mol.: 1 / Formula: C15H23NO4

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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: Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A
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, 45, 46, 47, 48
Buffer solutionDetails: Details can be retrieved from EMD-3227 / pH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R3/3

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Details: Details can be retrieved from EMD-3227.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDImaging ID
1SignaturePARTICLE SELECTION1
2EPU1.3IMAGE ACQUISITION1
4CTFFIND4CTF CORRECTION1
10RELION1.4INITIAL EULER ASSIGNMENT1
11RELION1.4FINAL EULER ASSIGNMENT1
13RELION1.4RECONSTRUCTION1
CTF correctionDetails: Each Particle / Type: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1
3D reconstructionMethod: Projection Matching / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 62532
Details: Computational sorting and classification was done in SPIDER, movie processing and high resolution refinement was done with RELION

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