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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 A resolution / 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

Nat. Struct. Mol. Biol., 2017 StrPapers
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

DateDeposition: Jul 26, 2016 / Release: Apr 12, 2017

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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 (A2)128260
ΔGint (kcal/M)-1033
Surface area (A2)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
#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
#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
#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
#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
#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
#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
#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
#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
#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
#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
#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
#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
#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
#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
#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
#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
#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

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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

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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 experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: 40S-ABCE1 complex / Type: RIBOSOME
Specimen supportGrid material: COPPER/PALLADIUM / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100

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Electron microscopy imaging

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 / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Processing

3D reconstructionResolution: 3.9 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 102000
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL

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