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- PDB-6wl5: Crystal structure of EcmrR C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 6wl5
TitleCrystal structure of EcmrR C-terminal domain
ComponentsEcmrR transcriptional regulator
KeywordsTRANSCRIPTION / Transcriptional factor
Function / homologyCETYL-TRIMETHYL-AMMONIUM
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.4 Å
AuthorsYang, Y. / Liu, C. / Liu, B.
CitationJournal: Nat Commun / Year: 2021
Title: Structural visualization of transcription activated by a multidrug-sensing MerR family regulator.
Authors: Yang Yang / Chang Liu / Wei Zhou / Wei Shi / Ming Chen / Baoyue Zhang / David G Schatz / Yangbo Hu / Bin Liu /
Abstract: Bacterial RNA polymerase (RNAP) holoenzyme initiates transcription by recognizing the conserved -35 and -10 promoter elements that are optimally separated by a 17-bp spacer. The MerR family of ...Bacterial RNA polymerase (RNAP) holoenzyme initiates transcription by recognizing the conserved -35 and -10 promoter elements that are optimally separated by a 17-bp spacer. The MerR family of transcriptional regulators activate suboptimal 19-20 bp spacer promoters in response to myriad cellular signals, ranging from heavy metals to drug-like compounds. The regulation of transcription by MerR family regulators is not fully understood. Here we report one crystal structure of a multidrug-sensing MerR family regulator EcmrR and nine cryo-electron microscopy structures that capture the EcmrR-dependent transcription process from promoter opening to initial transcription to RNA elongation. These structures reveal that EcmrR is a dual ligand-binding factor that reshapes the suboptimal 19-bp spacer DNA to enable optimal promoter recognition, sustains promoter remodeling to stabilize initial transcribing complexes, and finally dissociates from the promoter to reverse DNA remodeling and facilitate the transition to elongation. Our findings yield a comprehensive model for transcription regulation by MerR family factors and provide insights into the transition from transcription initiation to elongation.
History
DepositionApr 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: 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.title / _citation.year
Revision 1.2May 26, 2021Group: 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 / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EcmrR transcriptional regulator
B: EcmrR transcriptional regulator
C: EcmrR transcriptional regulator
D: EcmrR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,51930
Polymers73,4644
Non-polymers4,05626
Water17,457969
1
A: EcmrR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5018
Polymers18,3661
Non-polymers1,1357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EcmrR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2137
Polymers18,3661
Non-polymers8476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: EcmrR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5318
Polymers18,3661
Non-polymers1,1657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: EcmrR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2737
Polymers18,3661
Non-polymers9076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)212.393, 42.419, 115.798
Angle α, β, γ (deg.)90.000, 117.270, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
EcmrR transcriptional regulator


Mass: 18365.973 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 995 molecules

#2: Chemical
ChemComp-16A / CETYL-TRIMETHYL-AMMONIUM


Mass: 284.543 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C19H42N
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 969 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.16 Å3/Da / Density % sol: 61.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.5 M sodium chloride, 0.01 M magnesium chloride, 0.01 M cetyltrimethylammonium bromide

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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 PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.4→103.21 Å / Num. obs: 178379 / % possible obs: 98.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.032 / Rrim(I) all: 0.059 / Net I/σ(I): 12.4
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 17848 / CC1/2: 0.707 / Rpim(I) all: 0.382 / Rrim(I) all: 0.715 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.4→102.93 Å / SU ML: 0.1351 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.8585
RfactorNum. reflection% reflection
Rfree0.1728 8912 5 %
Rwork0.142 --
obs0.1435 178280 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.4 Å2
Refinement stepCycle: LAST / Resolution: 1.4→102.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 259 969 6376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01375880
X-RAY DIFFRACTIONf_angle_d1.46827966
X-RAY DIFFRACTIONf_chiral_restr0.0961829
X-RAY DIFFRACTIONf_plane_restr0.00921011
X-RAY DIFFRACTIONf_dihedral_angle_d20.0142301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.28043000.22535707X-RAY DIFFRACTION99.22
1.42-1.430.26872920.21445556X-RAY DIFFRACTION99.17
1.43-1.450.2612990.20565690X-RAY DIFFRACTION99.27
1.45-1.470.23933000.19085711X-RAY DIFFRACTION99.09
1.47-1.490.2382920.1885563X-RAY DIFFRACTION98.7
1.49-1.510.22762990.17245663X-RAY DIFFRACTION98.87
1.51-1.530.21882940.18235594X-RAY DIFFRACTION97.97
1.53-1.550.22912940.17015575X-RAY DIFFRACTION98.46
1.55-1.580.22252980.15875661X-RAY DIFFRACTION98.51
1.58-1.60.18682910.14135539X-RAY DIFFRACTION97.85
1.6-1.630.1812980.13265677X-RAY DIFFRACTION97.85
1.63-1.660.1842830.13335392X-RAY DIFFRACTION95.55
1.66-1.690.16623010.1235715X-RAY DIFFRACTION99.05
1.69-1.730.16192970.1175644X-RAY DIFFRACTION99.5
1.73-1.760.17193020.12055739X-RAY DIFFRACTION99.77
1.76-1.80.17682970.12175647X-RAY DIFFRACTION99.33
1.8-1.850.15423000.12245684X-RAY DIFFRACTION99.39
1.85-1.90.17212990.12385693X-RAY DIFFRACTION98.96
1.9-1.960.1572940.12555579X-RAY DIFFRACTION98.03
1.96-2.020.17093000.12565690X-RAY DIFFRACTION98.47
2.02-2.090.1632930.13025563X-RAY DIFFRACTION97.5
2.09-2.180.15362960.12415624X-RAY DIFFRACTION97.63
2.18-2.270.162860.12165437X-RAY DIFFRACTION94.63
2.27-2.390.15222910.11995535X-RAY DIFFRACTION96.25
2.39-2.540.16893030.13775754X-RAY DIFFRACTION99.7
2.54-2.740.16693010.13565716X-RAY DIFFRACTION99.13
2.74-3.020.15133050.13935797X-RAY DIFFRACTION99.27
3.02-3.450.15893020.14265723X-RAY DIFFRACTION98.93
3.45-4.350.16462930.13735580X-RAY DIFFRACTION95.22
4.35-102.930.1863120.18155920X-RAY DIFFRACTION98.1

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