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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
Components
  • (40S ribosomal protein ...) x 18
  • 18S ribosomal RNA
  • Translation initiation factor RLI1
KeywordsRIBOSOME / ABCE1 / recycling / 40S
Function / homology
Function and homology information


Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / ribosome disassembly / mTORC1-mediated signalling / Protein hydroxylation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition ...Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / ribosome disassembly / mTORC1-mediated signalling / Protein hydroxylation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit binding / 90S preribosome / Ub-specific processing proteases / 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) / regulation of translational fidelity / ribosomal subunit export from nucleus / translational termination / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of translation / small-subunit processome / translational initiation / maintenance of translational fidelity / rRNA processing / cytoplasmic stress granule / ribosome biogenesis / ribosomal small subunit assembly / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / iron ion binding / translation / mRNA binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2650 / Ribosomal protein S26 / Ribosomal protein S8e, subdomain / Ribosomal protein S4, central domain / Phosducin; domain 2 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S21 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2650 / Ribosomal protein S26 / Ribosomal protein S8e, subdomain / Ribosomal protein S4, central domain / Phosducin; domain 2 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S21 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / Alpha-Beta Plaits - #3370 / RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / Ribosomal Protein S8; Chain: A, domain 1 - #30 / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / S15/NS1, RNA-binding / RNA-binding S4 domain / SH3 type barrels. - #30 / 4Fe-4S binding domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Double Stranded RNA Binding Domain - #20 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / N-terminal domain of TfIIb / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Double Stranded RNA Binding Domain / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S8e subdomain, eukaryotes / : / Ribosomal protein S7e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S27e signature. / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S8e / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Single Sheet / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Dna Ligase; domain 1 / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A ...PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Small ribosomal subunit protein uS17A / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Small ribosomal subunit protein eS26A / Translation initiation factor RLI1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHeuer, A. / Gerovac, M. / Schmidt, C. / Trowitzsch, S. / Preis, A. / Koetter, P. / Berninghausen, O. / Becker, T. / Beckmann, R. / Tampe, R.
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: Structure of the 40S-ABCE1 post-splitting complex in ribosome recycling and translation initiation.
Authors: André Heuer / Milan Gerovac / Christian Schmidt / Simon Trowitzsch / Anne Preis / Peter Kötter / Otto Berninghausen / Thomas Becker / Roland Beckmann / Robert Tampé /
Abstract: The essential ATP-binding cassette protein ABCE1 splits 80S ribosomes into 60S and 40S subunits after canonical termination or quality-control-based mRNA surveillance processes. However, the ...The essential ATP-binding cassette protein ABCE1 splits 80S ribosomes into 60S and 40S subunits after canonical termination or quality-control-based mRNA surveillance processes. However, the underlying splitting mechanism remains enigmatic. Here, we present a cryo-EM structure of the yeast 40S-ABCE1 post-splitting complex at 3.9-Å resolution. Compared to the pre-splitting state, we observe repositioning of ABCE1's iron-sulfur cluster domain, which rotates 150° into a binding pocket on the 40S subunit. This repositioning explains a newly observed anti-association activity of ABCE1. Notably, the movement implies a collision with A-site factors, thus explaining the splitting mechanism. Disruption of key interactions in the post-splitting complex impairs cellular homeostasis. Additionally, the structure of a native post-splitting complex reveals ABCE1 to be part of the 43S initiation complex, suggesting a coordination of termination, recycling, and initiation.
History
DepositionJul 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.name
Revision 1.3Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Polymers989,93220
Non-polymers1,7405
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area128260 Å2
ΔGint-1033 kcal/mol
Surface area301710 Å2
MethodPISA

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Components

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

#2: Protein 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 method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32905
#3: Protein 40S ribosomal protein S1-A / RP10A / Small ribosomal subunit protein eS1-A


Mass: 28798.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P33442
#4: Protein 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 method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25443
#5: Protein 40S ribosomal protein S4-A / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6


Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX35
#6: Protein 40S ribosomal protein S6-A / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4


Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX37
#7: Protein 40S ribosomal protein S7-A / RP30 / RP40 / Small ribosomal subunit protein eS7-A


Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26786
#8: Protein 40S ribosomal protein S8-A / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9


Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX39
#9: Protein 40S ribosomal protein S9-A / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O13516
#10: Protein 40S ribosomal protein S11-A / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12


Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX47
#11: Protein 40S ribosomal protein S13 / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05756
#12: Protein 40S ribosomal protein S14-A / RP59A / Small ribosomal subunit protein uS11-A


Mass: 14562.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06367
#13: Protein 40S ribosomal protein S21-A / S26 / Small ribosomal subunit protein eS21-A / YS25


Mass: 9758.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0V8
#14: Protein 40S ribosomal protein S22-A / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22


Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W1
#15: Protein 40S ribosomal protein S23-A / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX29
#16: Protein 40S ribosomal protein S24-A / RP50 / Small ribosomal subunit protein eS24-A


Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX31
#17: Protein 40S ribosomal protein S26-A / Small ribosomal subunit protein eS26-A


Mass: 13538.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39938
#18: Protein 40S ribosomal protein S27-A / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8893.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35997
#19: Protein 40S ribosomal protein S30-A / Small ribosomal subunit protein eS30-A


Mass: 7137.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX33

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RNA chain / Protein , 2 types, 2 molecules 2h

#1: RNA chain 18S ribosomal RNA


Mass: 579126.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 874346701
#20: Protein Translation initiation factor RLI1 / ATP-binding cassette sub-family E member RLI1 / RNase L inhibitor


Mass: 68433.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03195

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Non-polymers , 3 types, 5 molecules

#21: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#22: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#23: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 40S-ABCE1 complex / Type: RIBOSOME / Entity ID: #1-#35 / Source: MULTIPLE SOURCES
Molecular weightValue: 1.2 MDa / Experimental value: YES
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
2100 mMPotassium acetateKOAc1
35 mMMagnesium acetateMgOAc1
4DithiothreitolDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Purified 40S ribosomal subunits were reconstituted with purified recombinantly expressed ABCE1
Specimen supportGrid material: COPPER/PALLADIUM / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: 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
IDNameVersionCategory
1Gautomatchparticle selection
2EM-Toolsimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13PHENIXmodel refinement
14REFMACmodel refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102000 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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