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- PDB-5lw7: S. solfataricus ABCE1 post-splitting state -

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Basic information

Entry
Database: PDB / ID: 5lw7
TitleS. solfataricus ABCE1 post-splitting state
ComponentsABC transporter ATP-binding protein
KeywordsRIBOSOME / ABCE1 / recycling / 30S
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / oxidoreductase activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / 4Fe-4S binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / ABC transporter-like, conserved site ...RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / 4Fe-4S binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / ABC transporter ATP-binding protein
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 17 Å
AuthorsHeuer, A. / Gerovac, M. / Beckmann, R. / Tampe, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFOR1805 Germany
CitationJournal: Nat Commun / Year: 2016
Title: Structure of the ribosome post-recycling complex probed by chemical cross-linking and mass spectrometry.
Authors: Kristin Kiosze-Becker / Alessandro Ori / Milan Gerovac / André Heuer / Elina Nürenberg-Goloub / Umar Jan Rashid / Thomas Becker / Roland Beckmann / Martin Beck / Robert Tampé /
Abstract: Ribosome recycling orchestrated by the ATP binding cassette (ABC) protein ABCE1 can be considered as the final-or the first-step within the cyclic process of protein synthesis, connecting translation ...Ribosome recycling orchestrated by the ATP binding cassette (ABC) protein ABCE1 can be considered as the final-or the first-step within the cyclic process of protein synthesis, connecting translation termination and mRNA surveillance with re-initiation. An ATP-dependent tweezer-like motion of the nucleotide-binding domains in ABCE1 transfers mechanical energy to the ribosome and tears the ribosome subunits apart. The post-recycling complex (PRC) then re-initiates mRNA translation. Here, we probed the so far unknown architecture of the 1-MDa PRC (40S/30S·ABCE1) by chemical cross-linking and mass spectrometry (XL-MS). Our study reveals ABCE1 bound to the translational factor-binding (GTPase) site with multiple cross-link contacts of the helix-loop-helix motif to the S24e ribosomal protein. Cross-linking of the FeS cluster domain to the ribosomal protein S12 substantiates an extreme lever-arm movement of the FeS cluster domain during ribosome recycling. We were thus able to reconstitute and structurally analyse a key complex in the translational cycle, resembling the link between translation initiation and ribosome recycling.
History
DepositionSep 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Derived calculations
Category: em_image_scans / em_software / pdbx_struct_conn_angle
Item: _em_software.name
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

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Assembly

Deposited unit
B: ABC transporter ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9903
Polymers67,2861
Non-polymers7032
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area730 Å2
ΔGint-47 kcal/mol
Surface area25850 Å2
MethodPISA

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Components

#1: Protein ABC transporter ATP-binding protein


Mass: 67286.273 Da / Num. of mol.: 1 / Mutation: E238A E485A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Gene: PAB0824 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UZA4
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4

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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: S. solfataricus ABCE1 post-splitting state / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.067 MDa / Experimental value: NO
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris pH 7.5Tris(hydroxymethyl)aminomethane1
2100 mMPotassium ChlorideKCl1
35 mMMgCl21
42 mMDTT1
SpecimenEmbedding 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 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI SPIRIT
Electron gunElectron source: OTHER / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 35000 nm / Calibrated defocus min: 10000 nm / Cs: 2.2 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k)

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Processing

EM software
IDNameVersionCategory
1Signatureparticle selection
2EM-Toolsimage acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
9Cootmodel refinement
10SPIDER9.03initial Euler assignment
11SPIDER9.03final Euler assignment
12SPIDER9.03classification
13SPIDER9.033D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 17 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 19500 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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