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- PDB-7o9h: Escherichia coli FtsY in complex with pppGpp -

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Basic information

Entry
Database: PDB / ID: 7o9h
TitleEscherichia coli FtsY in complex with pppGpp
ComponentsSignal recognition particle receptor FtsY
KeywordsTRANSLATION / stringent response / targeting complex / signal recognition particle / alarmones / stress
Function / homology
Function and homology information


SRP54, nucleotide-binding domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli DH5[alpha] (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 2.0Sep 27, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: 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 receptor FtsY
B: Signal recognition particle receptor FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9574
Polymers68,5912
Non-polymers1,3662
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-1 kcal/mol
Surface area26270 Å2
Unit cell
Length a, b, c (Å)74.480, 90.710, 106.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Signal recognition particle receptor FtsY / SRP receptor


Mass: 34295.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH5[alpha] (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7D5IKJ2
#2: Chemical ChemComp-0O2 / guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)


Mass: 683.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N5O20P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8.5% isopropanol, 0.085 M HEPES pH 7.5, 17% PEG 4000, 15 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.976253 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976253 Å / Relative weight: 1
ReflectionResolution: 2.4→45.35 Å / Num. obs: 161630 / % possible obs: 90.78 % / Redundancy: 6.2 % / Biso Wilson estimate: 34.12 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.85
Reflection shellResolution: 2.4→2.486 Å / Num. unique obs: 18544 / CC1/2: 0.782

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YHS

2yhs


Resolution: 2.4→45.35 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2593 1313 5 %
Rwork0.2033 --
obs0.2061 26248 90.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 0 80 87 4809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014797
X-RAY DIFFRACTIONf_angle_d1.226479
X-RAY DIFFRACTIONf_dihedral_angle_d16.076692
X-RAY DIFFRACTIONf_chiral_restr0.06750
X-RAY DIFFRACTIONf_plane_restr0.008826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50.3831570.3172987X-RAY DIFFRACTION100
2.5-2.610.32411580.2512994X-RAY DIFFRACTION100
2.61-2.750.3027930.2731767X-RAY DIFFRACTION59
2.75-2.920.27851580.2393004X-RAY DIFFRACTION100
2.92-3.140.27941590.21493025X-RAY DIFFRACTION100
3.14-3.460.27341340.21022553X-RAY DIFFRACTION84
3.46-3.960.27721230.20552334X-RAY DIFFRACTION76
3.96-4.990.20421620.16123074X-RAY DIFFRACTION100
4.99-45.350.22451690.1713197X-RAY DIFFRACTION99

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