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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
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 / recycling / 30S / ribosome
Specimen sourcePyrococcus abyssi (strain ge5 / orsay) / archaea / thermophilic
MethodElectron microscopy (17 Å resolution / Particle / Single particle)
AuthorsHeuer, A. / Gerovac, M. / Beckmann, R. / Tampe, R.
CitationNat Commun, 2016, 7, 13248-13248

Nat Commun, 2016, 7, 13248-13248 StrPapers
Structure of the ribosome post-recycling complex probed by chemical cross-linking and mass spectrometry.
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: Polypeptide(L)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 / thermophilic
References: UniProt: Q9UZA4

Molecular function

#2: ChemicalChemComp-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

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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 deg. / Units: MEGADALTONS / Experimental value: NO
Buffer solutionpH: 7.5
Buffer component
IDConc.UnitsNameFormulaBuffer ID
120mMTris pH 7.5Tris(hydroxymethyl)aminomethane1
2100mMPotassium ChlorideKCl1
35mMMgCl21
42mMDTT1
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 FIELD / 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
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1SignaturePARTICLE SELECTION1
2EM-ToolsIMAGE ACQUISITION1
4CTFFIND4CTF CORRECTION1
7UCSF ChimeraMODEL FITTING1
9CootMODEL REFINEMENT1
10SPIDER9.03INITIAL EULER ASSIGNMENT1
11SPIDER09.03FINAL EULER ASSIGNMENT1
12SPIDER09.03CLASSIFICATION1
13SPIDER09.03RECONSTRUCTION1
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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