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- PDB-8uvx: CosR DNA bound form I -

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Basic information

Entry
Database: PDB / ID: 8uvx
TitleCosR DNA bound form I
Components
  • DNA (5'-D(*AP*TP*AP*TP*CP*TP*TP*AP*AP*TP*TP*TP*TP*GP*GP*TP*TP*AP*AP*TP*A)-3')
  • DNA (5'-D(*TP*AP*TP*TP*AP*AP*CP*CP*AP*AP*AP*AP*TP*TP*AP*AP*GP*AP*TP*AP*T)-3')
  • DNA-binding response regulator
KeywordsDNA BINDING PROTEIN/DNA / CosR / transcriptional regulator / Campylobacter jejuni / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-binding response regulator
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhang, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: mBio / Year: 2024
Title: Structural basis of DNA recognition of the CosR regulator.
Authors: Zhemin Zhang / Yuqi Yan / Jinji Pang / Lei Dai / Qijing Zhang / Edward W Yu /
Abstract: is a foodborne pathogen commonly found in the intestinal tracts of animals. This pathogen is a leading cause of gastroenteritis in humans. Besides its highly infectious nature, is increasingly ... is a foodborne pathogen commonly found in the intestinal tracts of animals. This pathogen is a leading cause of gastroenteritis in humans. Besides its highly infectious nature, is increasingly resistant to a number of clinically administrated antibiotics. As a consequence, the Centers for Disease Control and Prevention has designated antibiotic-resistant as a serious antibiotic resistance threat in the United States. The CosR regulator is essential to the viability of this bacterium and is responsible for regulating the expression of a number of oxidative stress defense enzymes. Importantly, it also modulates the expression of the CmeABC multidrug efflux system, the most predominant and clinically important system in that mediates resistance to multiple antimicrobials. Here, we report structures of apo-CosR and CosR bound with a 21 bp DNA sequence located at the promotor region using both single-particle cryo-electron microscopy and X-ray crystallography. These structures allow us to propose a novel mechanism for CosR regulation that involves a long-distance conformational coupling and rearrangement of the secondary structural elements of the regulator to bind target DNA.
IMPORTANCE: has emerged as an antibiotic-resistant threat worldwide. CosR is an essential regulator for this bacterium and is important for adaptation to various stresses. Here, we describe the ...IMPORTANCE: has emerged as an antibiotic-resistant threat worldwide. CosR is an essential regulator for this bacterium and is important for adaptation to various stresses. Here, we describe the structural basis of CosR binding to target DNA as determined by cryo-electron microscopy and X-ray crystallography. Since CosR is a potential target for intervention, our studies may facilitate the development of novel therapeutics to combat infection.
History
DepositionNov 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA-binding response regulator
A: DNA-binding response regulator
C: DNA (5'-D(*AP*TP*AP*TP*CP*TP*TP*AP*AP*TP*TP*TP*TP*GP*GP*TP*TP*AP*AP*TP*A)-3')
D: DNA (5'-D(*TP*AP*TP*TP*AP*AP*CP*CP*AP*AP*AP*AP*TP*TP*AP*AP*GP*AP*TP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)63,8874
Polymers63,8874
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.125, 81.303, 68.073
Angle α, β, γ (deg.)90.000, 106.140, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein DNA-binding response regulator


Mass: 25504.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: hsrA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3H9R6A1
#2: DNA chain DNA (5'-D(*AP*TP*AP*TP*CP*TP*TP*AP*AP*TP*TP*TP*TP*GP*GP*TP*TP*AP*AP*TP*A)-3')


Mass: 6441.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Campylobacter jejuni (Campylobacter)
#3: DNA chain DNA (5'-D(*TP*AP*TP*TP*AP*AP*CP*CP*AP*AP*AP*AP*TP*TP*AP*AP*GP*AP*TP*AP*T)-3')


Mass: 6437.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Campylobacter jejuni (Campylobacter)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.02 M Sodium formate, 0.02 M Ammonium acetate, 0.02 M Sodiumcitrate, 0.02 M Sodiium potassium tartrate, 0.02 M Sodium oxamate, 0.01 M MES ph6.5, 40% v/v PEG 500 MME, 20% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 13804 / % possible obs: 87.67 % / Redundancy: 6.9 % / Biso Wilson estimate: 45.54 Å2 / CC1/2: 0.98 / Net I/σ(I): 10.14
Reflection shellResolution: 2.9→3.004 Å / Num. unique obs: 782 / CC1/2: 0.898

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→45 Å / SU ML: 0.4165 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 28.3278
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2679 1381 10 %
Rwork0.2412 12423 -
obs0.2439 13804 87.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.86 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 853 0 7 4217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824370
X-RAY DIFFRACTIONf_angle_d1.09926125
X-RAY DIFFRACTIONf_chiral_restr0.0474721
X-RAY DIFFRACTIONf_plane_restr0.0048650
X-RAY DIFFRACTIONf_dihedral_angle_d21.2531637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-30.4369730.3898679X-RAY DIFFRACTION47.78
3-3.120.4298990.3557958X-RAY DIFFRACTION67.54
3.12-3.260.32041160.31221067X-RAY DIFFRACTION76.03
3.26-3.430.30891440.29951269X-RAY DIFFRACTION90.06
3.43-3.650.31731500.27581408X-RAY DIFFRACTION98.8
3.65-3.930.27421590.24031400X-RAY DIFFRACTION99.43
3.93-4.330.2641590.22151397X-RAY DIFFRACTION99.17
4.33-4.950.23531580.20451378X-RAY DIFFRACTION97.4
4.95-6.230.24371570.22611450X-RAY DIFFRACTION99.5
6.24-450.20171660.18211417X-RAY DIFFRACTION98.08
Refinement TLS params.Method: refined / Origin x: 16.0855716936 Å / Origin y: 13.4967319751 Å / Origin z: -1.68664532314 Å
111213212223313233
T0.194565390237 Å2-0.0599519501788 Å20.00837067291504 Å2-0.223332265888 Å2-0.0316208873381 Å2--0.241426174789 Å2
L0.039869544057 °2-0.0277044363393 °2-0.159102857186 °2--0.0111381496738 °2-0.151760501097 °2--0.873626004137 °2
S0.0824500047913 Å °0.0517656713492 Å °0.0193021617699 Å °0.0301607985095 Å °0.023109701133 Å °-0.0273008059104 Å °0.0679094404848 Å °-0.302207612506 Å °-0.0899205347603 Å °
Refinement TLS groupSelection details: all

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