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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 / ribosome / recycling / 40S
Function / homologyRibosomal protein S15P / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S4/S9 / Ribosomal protein S2, flavodoxin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S11, N-terminal / Ribosomal protein S5 domain 2-type fold ...Ribosomal protein S15P / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S4/S9 / Ribosomal protein S2, flavodoxin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S11, N-terminal / Ribosomal protein S5 domain 2-type fold / RLI, domain 1 / Ribosomal protein S8 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S26e superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S17, conserved site / 4Fe-4S binding domain / Ribosomal protein S4, conserved site / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / ABC transporter, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Ribosomal S24e conserved site / Ribosomal protein S8e, conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / ABC transporter / Ribosomal protein S12/S23 / Ribosomal protein S26e signature. / Ribosomal protein S12 signature. / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / Ribosomal protein S17 signature. / Possible Fer4-like domain in RNase L inhibitor, RLI / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / ABC transporters family signature. / Ribosomal protein S15 signature. / Ribosomal protein S4e signature. / Ribosomal protein S24e signature. / Ribosomal protein S6e signature. / Ribosomal protein S5 signature. / Ribosomal protein S30 / Ribosomal protein S5, C-terminal domain / Ribosomal protein S15 / Ribosomal family S4e / Ribosomal protein S2 / Ribosomal protein S5, N-terminal domain / Ribosomal protein S17 / Ribosomal protein S8 / Ribosomal protein S11 / KOW motif / Ribosomal S3Ae family / Ribosomal protein S27 / Ribosomal protein S6e / Ribosomal protein S8e / Ribosomal protein S21e / Ribosomal protein S7e / Ribosomal protein S24e / Ribosomal protein S26e / S4 domain / Ribosomal protein S4e, central region / Ribosomal protein S4e, N-terminal / Ribosomal protein S5, N-terminal / ATP-binding cassette, ABC transporter-type domain profile. / Ribosomal protein S15 / Ribosomal protein S7e / Ribosomal protein S17/S11 / Ribosomal protein S7e signature. / RLI1 / Ribosomal protein S2 signature 2. / Ribosomal protein S21e signature. / Ribosomal protein S27e signature. / Ribosomal protein S3Ae signature. / Ribosomal protein S8e signature. / S5 double stranded RNA-binding domain profile. / S4 RNA-binding domain profile. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / Ribosomal protein S8 / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling / SRP-dependent cotranslational protein targeting to membrane / RMTs methylate histone arginines / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
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
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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Structure visualization

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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 PQRSTUVWXYZabcdefg

#2: Protein/peptide 40S ribosomal protein S0-A / Ribosome / Nucleic acid-binding protein NAB1A / Small ribosomal subunit protein uS2-A


Mass: 28051.330 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32905
#3: Protein/peptide 40S ribosomal protein S1-A / Ribosome / RP10A / Small ribosomal subunit protein eS1-A


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 15362.848 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX31
#17: Protein/peptide 40S ribosomal protein S26-A / Ribosome / Small ribosomal subunit protein eS26-A


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


Mass: 8893.391 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P35997
#19: Protein/peptide 40S ribosomal protein S30-A / Ribosome / Small ribosomal subunit protein eS30-A


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

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

#1: RNA chain 18S ribosomal RNA /


Mass: 579126.562 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 874346701
#20: Protein/peptide 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 (baker'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 / Formula: Fe4S4 / Iron–sulfur cluster
#22: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


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


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

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Experimental details

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Experiment

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

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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 MDa / Experimental value: YES
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer ID
120 mMHEPES1
2100 mMPotassium acetateKOAc1
35 mMMagnesium 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 FIELDBright-field microscopy / 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
9RELION2.0initial Euler assignment
10RELION2.0final Euler assignment
11RELION2.0classification
12RELION2.03D reconstruction
13PHENIXmodel refinement
14REFMACmodel refinement
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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