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Open data
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Basic information
Entry | Database: PDB / ID: 7o9i | |||||||||
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Title | Escherichia coli Ffh in complex with pppGpp | |||||||||
![]() | Signal recognition particle protein | |||||||||
![]() | TRANSLATION / stringent response / targeting complex / signal recognition particle / alarmones / stress | |||||||||
Function / homology | ![]() signal recognition particle / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane, translocation / protein targeting to membrane / ribonucleoprotein complex / GTPase activity / GTP binding / ATP hydrolysis activity / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Czech, L. / Mais, C.-N. / Bange, G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibition of SRP-dependent protein secretion by the bacterial alarmone (p)ppGpp. Authors: Laura Czech / Christopher-Nils Mais / Hanna Kratzat / Pinku Sarmah / Pietro Giammarinaro / Sven-Andreas Freibert / Hanna Folke Esser / Joanna Musial / Otto Berninghausen / Wieland Steinchen ...Authors: Laura Czech / Christopher-Nils Mais / Hanna Kratzat / Pinku Sarmah / Pietro Giammarinaro / Sven-Andreas Freibert / Hanna Folke Esser / Joanna Musial / Otto Berninghausen / Wieland Steinchen / Roland Beckmann / Hans-Georg Koch / Gert Bange / ![]() Abstract: The stringent response enables bacteria to respond to nutrient limitation and other stress conditions through production of the nucleotide-based second messengers ppGpp and pppGpp, collectively known ...The stringent response enables bacteria to respond to nutrient limitation and other stress conditions through production of the nucleotide-based second messengers ppGpp and pppGpp, collectively known as (p)ppGpp. Here, we report that (p)ppGpp inhibits the signal recognition particle (SRP)-dependent protein targeting pathway, which is essential for membrane protein biogenesis and protein secretion. More specifically, (p)ppGpp binds to the SRP GTPases Ffh and FtsY, and inhibits the formation of the SRP receptor-targeting complex, which is central for the coordinated binding of the translating ribosome to the SecYEG translocon. Cryo-EM analysis of SRP bound to translating ribosomes suggests that (p)ppGpp may induce a distinct conformational stabilization of the NG domain of Ffh and FtsY in Bacillus subtilis but not in E. coli. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.8 KB | Display | ![]() |
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PDB format | ![]() | 49.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 778.9 KB | Display | ![]() |
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Full document | ![]() | 783.9 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o5bC ![]() 7o9fC ![]() 7o9gC ![]() 7o9hC ![]() 3ng1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33395.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: ffh, b2610, JW5414 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-0O2 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.2 M sodium chloride, 0.1 M CHES pH 9.5, 50% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976253 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→41.05 Å / Num. obs: 11747 / % possible obs: 99.56 % / Redundancy: 19.2 % / CC1/2: 0.999 / Net I/σ(I): 25.77 |
Reflection shell | Resolution: 2.49→2.58 Å / Redundancy: 14.4 % / Num. unique obs: 1112 / CC1/2: 0.969 / % possible all: 96.29 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NG1 Resolution: 2.49→41.05 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 33.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→41.05 Å
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LS refinement shell |
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