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- PDB-4urd: Cryo-EM map of Trigger Factor bound to a translating ribosome -

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Entry
Database: PDB / ID: 4urd
TitleCryo-EM map of Trigger Factor bound to a translating ribosome
ComponentsTRIGGER FACTOR
KeywordsISOMERASE / TRANSLATION / CO-TRANSLATIONAL PROTEIN FOLDING
Function / homologyTrigger factor / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Bacterial trigger factor protein (TF) C-terminus / Bacterial trigger factor protein (TF) / FKBP-type peptidyl-prolyl cis-trans isomerase / Trigger factor, C-terminal domain superfamily / Trigger factor ribosome-binding domain superfamily / Trigger factor/SurA domain superfamily / Trigger factor, ribosome-binding, bacterial / Trigger factor, C-terminal ...Trigger factor / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Bacterial trigger factor protein (TF) C-terminus / Bacterial trigger factor protein (TF) / FKBP-type peptidyl-prolyl cis-trans isomerase / Trigger factor, C-terminal domain superfamily / Trigger factor ribosome-binding domain superfamily / Trigger factor/SurA domain superfamily / Trigger factor, ribosome-binding, bacterial / Trigger factor, C-terminal / FKBP-type peptidyl-prolyl cis-trans isomerase domain / 'de novo' cotranslational protein folding / protein folding chaperone / protein unfolding / chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosome binding / protein transport / response to heat / cell cycle / cell division / membrane / identical protein binding / cytosol / un:i4uk46: / Trigger factor
Function and homology information
Specimen sourceESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 7.7 Å resolution
AuthorsDeeng, J. / Chan, K.Y. / van der Sluis, E. / Bischoff, L. / Berninghausen, O. / Han, W. / Gumbart, J. / Schulten, K. / Beatrix, B. / Beckmann, R.
CitationJournal: J. Mol. Biol. / Year: 2016
Title: Dynamic Behavior of Trigger Factor on the Ribosome.
Authors: J Deeng / K Y Chan / E O van der Sluis / O Berninghausen / W Han / J Gumbart / K Schulten / B Beatrix / R Beckmann
Abstract: Trigger factor (TF) is the only ribosome-associated chaperone in bacteria. It interacts with hydrophobic segments in nascent chain (NCs) as they emerge from the ribosome. TF binds via its N-terminal ...Trigger factor (TF) is the only ribosome-associated chaperone in bacteria. It interacts with hydrophobic segments in nascent chain (NCs) as they emerge from the ribosome. TF binds via its N-terminal ribosome-binding domain (RBD) mainly to ribosomal protein uL23 at the tunnel exit on the large ribosomal subunit. Whereas earlier structural data suggested that TF binds as a rigid molecule to the ribosome, recent comparisons of structural data on substrate-bound, ribosome-bound, and TF in solution from different species suggest that this chaperone is a rather flexible molecule. Here, we present two cryo-electron microscopy structures of TF bound to ribosomes translating an mRNA coding for a known TF substrate from Escherichia coli of a different length. The structures reveal distinct degrees of flexibility for the different TF domains, a conformational rearrangement of the RBD upon ribosome binding, and an increase in rigidity within TF when the NC is extended. Molecular dynamics simulations agree with these data and offer a molecular basis for these observations.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 27, 2014 / Release: Jan 13, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 13, 2016Structure modelrepositoryInitial release
1.1Jun 22, 2016Structure modelDatabase references
1.2Jun 29, 2016Structure modelDatabase references
1.3Oct 5, 2016Structure modelDatabase references
1.4Oct 3, 2018Structure modelData collectionem_software_em_software.image_processing_id

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Assembly

Deposited unit
A: TRIGGER FACTOR


Theoretical massNumber of molelcules
Total (without water)12,7121
Polyers12,7121
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein/peptide TRIGGER FACTOR


Mass: 12711.546 Da / Num. of mol.: 1 / Fragment: RIBOSOME BINDING DOMAIN, RESIDUES 1-115 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: I4UK46, UniProt: P0A850*PLUS

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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: TNAC-STALLED-RNC WITH TRIGGER FACTOR / Type: COMPLEX
Buffer solutionName: 20 MM HEPES, 100 MM KOAC, 10 MM MG(OAC)2, 2 MM DTT / Details: 20 MM HEPES, 100 MM KOAC, 10 MM MG(OAC)2, 2 MM DTT / pH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT FOR 10 SECONDS BEFORE PLUNGING, USE 2 LAYERS OF FILTER PAPER V,

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30 / Date: Nov 21, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 / Calibrated magnification: 38900 / Nominal defocus max: 3500 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 221

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: ON VOLUMES (SPIDER)
SymmetryPoint symmetry: C1
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 7.7 Å / Number of particles: 100931
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2695. (DEPOSITION ID: 12641).
Symmetry type: POINT
Least-squares processHighest resolution: 7.7 Å
Refine hist #LASTHighest resolution: 7.7 Å
Number of atoms included #LASTProtein: 893 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 893

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