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

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Basic information

Entry
Database: PDB / ID: 4urd
TitleCryo-EM map of Trigger Factor bound to a translating ribosome
DescriptorTRIGGER FACTOR
KeywordsISOMERASE / TRANSLATION / CO-TRANSLATIONAL PROTEIN FOLDING
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (7.7 Å resolution / Particle / Single particle)
AuthorsDeeng, J. / Chan, K.Y. / van der Sluis, E. / Bischoff, L. / Berninghausen, O. / Han, W. / Gumbart, J. / Schulten, K. / Beatrix, B. / Beckmann, R.
CitationJ. Mol. Biol., 2016, 428, 3588-3602

J. Mol. Biol., 2016, 428, 3588-3602 StrPapers
Dynamic Behavior of Trigger Factor on the Ribosome.
J Deeng / K Y Chan / E O van der Sluis / O Berninghausen / W Han / J Gumbart / K Schulten / B Beatrix / R Beckmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 27, 2014 / Release: Jan 13, 2016
RevisionDateData content typeGroupProviderType
1.0Jan 13, 2016Structure modelrepositoryInitial release
1.1Jun 22, 2016Structure modelDatabase references
1.2Jun 29, 2016Structure modelDatabase references
1.3Oct 5, 2016Structure modelDatabase references

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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: Polypeptide(L)TRIGGER FACTOR


Mass: 12711.546 Da / Num. of mol.: 1 / Fragment: RIBOSOME BINDING DOMAIN, RESIDUES 1-115
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: I4UK46

Cellular component

Molecular function

Biological process

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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: 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 FIELD / 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: 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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