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- PDB-7o9g: Escherichia coli Ffh in complex with ppGpp -

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Basic information

Entry
Database: PDB / ID: 7o9g
TitleEscherichia coli Ffh in complex with ppGpp
ComponentsSignal recognition particle protein
KeywordsTRANSLATION / stringent response / targeting complex / signal recognition particle / alarmones / stress
Function / homology
Function and homology information


signal recognition particle / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / GTPase activity / GTP binding
Similarity search - Function
Signal recognition particle protein / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain ...Signal recognition particle protein / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / Signal recognition particle protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCzech, L. / Mais, C.-N. / Bange, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1879 Germany
CitationJournal: Nat Commun / Year: 2022
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
DepositionApr 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal recognition particle protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0233
Polymers33,3951
Non-polymers6272
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-16 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.630, 38.200, 78.440
Angle α, β, γ (deg.)90.00, 96.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Signal recognition particle protein / Fifty-four homolog


Mass: 33395.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ffh, BANRA_03474 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3P5DUI2
#2: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium acetate, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.8→43.26 Å / Num. obs: 7083 / % possible obs: 97.41 % / Redundancy: 3.4 % / CC1/2: 0.999 / Net I/σ(I): 32.05
Reflection shellResolution: 2.803→2.904 Å / Num. unique obs: 698 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Cootmodel building
XSCALEdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NG1

3ng1


Resolution: 2.8→43.26 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2598 355 5.02 %
Rwork0.1919 --
obs0.1952 7077 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→43.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 37 9 2283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112308
X-RAY DIFFRACTIONf_angle_d1.6353129
X-RAY DIFFRACTIONf_dihedral_angle_d23.853316
X-RAY DIFFRACTIONf_chiral_restr0.066371
X-RAY DIFFRACTIONf_plane_restr0.008401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.210.38141160.26832202X-RAY DIFFRACTION97
3.21-4.040.30891180.20272228X-RAY DIFFRACTION98
4.04-43.260.19721210.16452292X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -1.6324 Å / Origin y: 0.2404 Å / Origin z: 18.5 Å
111213212223313233
T0.4616 Å20.0436 Å20.0212 Å2-0.4445 Å2-0.0292 Å2--0.4077 Å2
L1.1272 °20.3838 °20.9713 °2-0.8143 °20.0347 °2--0.8791 °2
S0.0323 Å °-0.0827 Å °-0.1442 Å °0.0354 Å °0.0532 Å °-0.1036 Å °0.0151 Å °-0.036 Å °0.0001 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 3 through 296)

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