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- PDB-5ll6: Structure of the 40S ABCE1 post-splitting complex in ribosome rec... -

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Entry
Database: PDB / ID: 5ll6
TitleStructure of the 40S ABCE1 post-splitting complex in ribosome recycling and translation initiation
DescriptorUbiquitin-40S ribosomal protein S31
Guanine nucleotide-binding protein subunit beta-like protein
Translation initiation factor RLI1/RNA Complex
(40S ribosomal protein ...) x 31
KeywordsRIBOSOME / ABCE1 / ribosome / recycling / 40S
Specimen sourceSaccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
MethodElectron microscopy (3.9 Å resolution / Particle / Single particle)
AuthorsHeuer, A. / Gerovac, M. / Schmidt, C. / Trowitzsch, S. / Preis, A. / Koetter, P. / Berninghausen, O. / Becker, T. / Beckmann, R. / Tampe, R.
CitationNat. Struct. Mol. Biol., 2017, 24, 453-460

Nat. Struct. Mol. Biol., 2017, 24, 453-460 Yorodumi Papers
Structure of the 40S-ABCE1 post-splitting complex in ribosome recycling and translation initiation.
André Heuer / Milan Gerovac / Christian Schmidt / Simon Trowitzsch / Anne Preis / Peter Kötter / Otto Berninghausen / Thomas Becker / Roland Beckmann / Robert Tampé

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 26, 2016 / Release: Apr 12, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 12, 2017Structure modelrepositoryInitial release
1.1May 17, 2017Structure modelDatabase references
1.2Aug 30, 2017Structure modelData collectionem_image_scans / em_software_em_software.name

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Assembly

Deposited unit
2: 18S ribosomal RNA
P: 40S ribosomal protein S0-A
Q: 40S ribosomal protein S1-A
R: 40S ribosomal protein S2
S: 40S ribosomal protein S4-A
T: 40S ribosomal protein S6-A
U: 40S ribosomal protein S7-A
V: 40S ribosomal protein S8-A
W: 40S ribosomal protein S9-A
X: 40S ribosomal protein S11-A
Y: 40S ribosomal protein S13
Z: 40S ribosomal protein S14-A
a: 40S ribosomal protein S21-A
b: 40S ribosomal protein S22-A
c: 40S ribosomal protein S23-A
d: 40S ribosomal protein S24-A
e: 40S ribosomal protein S26-A
f: 40S ribosomal protein S27-A
g: 40S ribosomal protein S30-A
h: Translation initiation factor RLI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)991,67225
Polyers989,93220
Non-polymers1,7405
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)128260
ΔGint (kcal/M)-1033
Surface area (Å2)301710
MethodPISA

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Components

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40S ribosomal protein ... , 18 types, 18 molecules PQRSTUVWXY...

#2: Polypeptide(L)40S ribosomal protein S0-A / Nucleic acid-binding protein NAB1A / Small ribosomal subunit protein uS2-A


Mass: 28051.330 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P32905

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000447)
  • endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000461)
  • ribosomal small subunit assembly (GO: 0000028)
  • rRNA export from nucleus (GO: 0006407)
#3: Polypeptide(L)40S ribosomal protein S1-A / RP10A / Small ribosomal subunit protein eS1-A


Mass: 28798.467 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P33442

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
#4: Polypeptide(L)40S ribosomal protein S2 / Omnipotent suppressor protein SUP44 / RP12 / S4 / Small ribosomal subunit protein uS5 / YS5


Mass: 27490.826 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P25443

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)40S ribosomal protein S4-A / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6


Mass: 29469.330 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX35

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)40S ribosomal protein S6-A / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4


Mass: 27054.486 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX37

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • rRNA methylation (GO: 0031167)
#7: Polypeptide(L)40S ribosomal protein S7-A / RP30 / RP40 / Small ribosomal subunit protein eS7-A


Mass: 21658.209 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P26786

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)40S ribosomal protein S8-A / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9


Mass: 22537.803 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX39

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
#9: Polypeptide(L)40S ribosomal protein S9-A / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: O13516

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • positive regulation of translational fidelity (GO: 0045903)
  • rRNA methylation (GO: 0031167)
#10: Polypeptide(L)40S ribosomal protein S11-A / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12


Mass: 17785.934 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX47

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)40S ribosomal protein S13 / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P05756

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)40S ribosomal protein S14-A / RP59A / Small ribosomal subunit protein uS11-A


Mass: 14562.655 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P06367

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)40S ribosomal protein S21-A / S26 / Small ribosomal subunit protein eS21-A / YS25


Mass: 9758.829 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0C0V8

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000447)
  • endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000461)
#14: Polypeptide(L)40S ribosomal protein S22-A / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22


Mass: 14650.062 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0C0W1

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)40S ribosomal protein S23-A / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


Mass: 16073.896 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX29

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • regulation of translational fidelity (GO: 0006450)
  • translation (GO: 0006412)
#16: Polypeptide(L)40S ribosomal protein S24-A / RP50 / Small ribosomal subunit protein eS24-A


Mass: 15362.848 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX31

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
#17: Polypeptide(L)40S ribosomal protein S26-A / Small ribosomal subunit protein eS26-A


Mass: 13538.922 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P39938

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)40S ribosomal protein S27-A / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8893.391 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P35997

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)40S ribosomal protein S30-A / Small ribosomal subunit protein eS30-A


Mass: 7137.541 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CX33

Cellular component

Molecular function

Biological process

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RNA chain / Polypeptide(L) , 2 types, 2 molecules 2h

#1: RNA chain18S ribosomal RNA


Mass: 579126.562 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: 874346701
#20: Polypeptide(L)Translation initiation factor RLI1 / ATP-binding cassette sub-family E member RLI1 / RNase L inhibitor


Mass: 68433.242 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q03195

Cellular component

Molecular function

Biological process

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Non-polymers , 3 types, 5 molecules

#21: ChemicalChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Formula: Fe4S4
#22: ChemicalChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP (energy-carrying molecule analogue) *YM


Mass: 506.196 Da / Num. of mol.: 2 / Formula: C10H17N6O12P3
#23: ChemicalChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg

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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: 40S-ABCE1 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
Source: MULTIPLE SOURCES
Molecular weightValue: 1.2 deg. / Units: MEGADALTONS / Experimental value: YES
Buffer solutionpH: 7.4
Buffer component
IDConc.UnitsNameFormulaBuffer ID
120mMHEPES1
2100mMPotassium acetateKOAc1
35mMMagnesium acetateMgOAc1
4DithiothreitolDTT1
SpecimenDetails: Purified 40S ribosomal subunits were reconstituted with purified recombinantly expressed ABCE1
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/PALLADIUM / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 kelvins

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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 / Nominal defocus max: 2400 nm / Calibrated defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2.4 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1GautomatchPARTICLE SELECTION1
2EM-ToolsIMAGE ACQUISITION1
4CTFFIND4CTF CORRECTION1
7CootMODEL FITTING1
9RELION2.0INITIAL EULER ASSIGNMENT1
10RELION2.0FINAL EULER ASSIGNMENT1
11RELION2.0CLASSIFICATION1
12RELION2.0RECONSTRUCTION1
13PHENIXMODEL REFINEMENT1
14REFMACMODEL REFINEMENT1
CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 102000 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL

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