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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 / ribosome
Function / homology4Fe-4S ferredoxin, iron-sulphur binding, conserved site / ATP-binding cassette, ABC transporter-type domain profile. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Possible Fer4-like domain in RNase L inhibitor, RLI / 4Fe-4S binding domain / ABC transporter / RLI, domain 1 / P-loop containing nucleoside triphosphate hydrolase / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / ABC transporter, conserved site ...4Fe-4S ferredoxin, iron-sulphur binding, conserved site / ATP-binding cassette, ABC transporter-type domain profile. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Possible Fer4-like domain in RNase L inhibitor, RLI / 4Fe-4S binding domain / ABC transporter / RLI, domain 1 / P-loop containing nucleoside triphosphate hydrolase / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / ABC transporter, conserved site / RLI1 / RNase L inhibitor RLI, possible metal-binding domain / AAA+ ATPase domain / ABC transporter-like / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / ABC transporters family signature. / 4 iron, 4 sulfur cluster binding / ATPase activity / ATP binding / metal ion binding / ABC transporter ATP-binding protein
Function and homology information
Specimen sourcePyrococcus abyssi (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 17 Å resolution
AuthorsHeuer, A. / Gerovac, M. / Beckmann, R. / Tampe, R.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 15, 2016 / Release: Nov 16, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 16, 2016Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collection / Derived calculationsem_image_scans / em_software / pdbx_struct_conn_angle_em_software.name

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,9903
Polyers67,2861
Non-polymers7032
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)730
ΔGint (kcal/M)-47
Surface area (Å2)25850
MethodPISA

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Components

#1: Protein/peptide ABC transporter ATP-binding protein


Mass: 67286.273 Da / Num. of mol.: 1 / Mutation: E238A E485A
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


Mass: 351.640 Da / Num. of mol.: 2 / Formula: Fe4S4

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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: 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 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
MicroscopyMicroscope model: 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
11SPIDER09.03final Euler assignment
12SPIDER09.03classification
13SPIDER09.033D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 17 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 19500 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT

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