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- PDB-8cwt: Complex structure of WhiB3 and the SigmaAr4-RNAP Beta flap tip ch... -

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Basic information

Entry
Database: PDB / ID: 8cwt
TitleComplex structure of WhiB3 and the SigmaAr4-RNAP Beta flap tip chimera in space group P43212
Components
  • RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta
  • Redox- and pH-responsive transcriptional regulator WhiB3
KeywordsTRANSCRIPTION / redox sensor / transcriptional factor
Function / homology
Function and homology information


response to host redox environment / Actinobacterium-type cell wall biogenesis / response to water / dinitrosyl-iron complex binding / Antimicrobial action and antimicrobial resistance in Mtb / protein-disulfide reductase [NAD(P)H] activity / iron-sulfur cluster binding / sigma factor activity / regulation of lipid metabolic process / protein-disulfide reductase activity ...response to host redox environment / Actinobacterium-type cell wall biogenesis / response to water / dinitrosyl-iron complex binding / Antimicrobial action and antimicrobial resistance in Mtb / protein-disulfide reductase [NAD(P)H] activity / iron-sulfur cluster binding / sigma factor activity / regulation of lipid metabolic process / protein-disulfide reductase activity / DNA-directed RNA polymerase complex / cell redox homeostasis / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / 4 iron, 4 sulfur cluster binding / response to antibiotic / negative regulation of DNA-templated transcription / DNA-templated transcription / DNA binding / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Transcription factor WhiB / WhiB-like iron-sulfur binding domain / Transcription factor WhiB / 4Fe-4S WhiB-like (Wbl)-type iron-sulfur binding domain profile. / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 ...Transcription factor WhiB / WhiB-like iron-sulfur binding domain / Transcription factor WhiB / 4Fe-4S WhiB-like (Wbl)-type iron-sulfur binding domain profile. / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / DNA-directed RNA polymerase beta subunit, bacterial-type / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / IRON/SULFUR CLUSTER / Redox- and pH-responsive transcriptional regulator WhiB3 / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsWan, T. / Zhang, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM138157-01 United States
National Science Foundation (NSF, United States)CLP 1846908 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis.
Authors: Wan, T. / Horova, M. / Khetrapal, V. / Li, S. / Jones, C. / Schacht, A. / Sun, X. / Zhang, L.
History
DepositionMay 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Redox- and pH-responsive transcriptional regulator WhiB3
B: RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta
C: Redox- and pH-responsive transcriptional regulator WhiB3
D: RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta
E: Redox- and pH-responsive transcriptional regulator WhiB3
F: RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,99044
Polymers68,7576
Non-polymers4,23438
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18660 Å2
ΔGint-536 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.826, 121.826, 114.305
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Redox- and pH-responsive transcriptional regulator WhiB3


Mass: 10268.640 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: whiB3, Rv3416 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WF41
#2: Protein RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta / Sigma-A / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 12650.234 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The last 82 residues in the C-terminal of the primary sigma factor was fused with the flap tip helix (T815-A829) from RNA polymerase beta subunit, with six histidine tag at the N-terminus
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv
Gene: sigA, mysA, rpoD, rpoV, Rv2703, MTCY05A6.24, rpoB, Rv0667, MTCI376.08c
Production host: Escherichia coli (E. coli)
References: UniProt: P9WGI1, UniProt: P9WGY9, DNA-directed RNA polymerase

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Non-polymers , 5 types, 560 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.11 Å3/Da / Density % sol: 60.5 % / Description: Large rhombus crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 10-20 mM NiCl2, 0.8-1.0 M Li2SO4 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: Collected under liquid nitrogen stream
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 187184 / % possible obs: 99.9 % / Redundancy: 25.3 % / Biso Wilson estimate: 19.68 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.016 / Rrim(I) all: 0.083 / Χ2: 0.885 / Net I/σ(I): 48.2
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 24.7 % / Rmerge(I) obs: 3.02 / Num. unique obs: 18429 / CC1/2: 0.66 / CC star: 0.89 / Rpim(I) all: 0.619 / Rrim(I) all: 3.08 / Χ2: 0.494 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-3000v1.0data reduction
HKL-3000v1.0data scaling
AutoSolv1.0phasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→41.68 Å / SU ML: 0.1287 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.0755
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1739 9185 4.91 %
Rwork0.1517 177986 -
obs0.1528 187171 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.1 Å2
Refinement stepCycle: LAST / Resolution: 1.35→41.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4400 0 180 522 5102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01244990
X-RAY DIFFRACTIONf_angle_d1.67356833
X-RAY DIFFRACTIONf_chiral_restr0.1243712
X-RAY DIFFRACTIONf_plane_restr0.0108887
X-RAY DIFFRACTIONf_dihedral_angle_d22.97921971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.360.27572860.26645815X-RAY DIFFRACTION98.83
1.36-1.380.27943100.26225883X-RAY DIFFRACTION99.98
1.38-1.40.23042950.23765839X-RAY DIFFRACTION100
1.4-1.420.23893190.21685911X-RAY DIFFRACTION100
1.42-1.430.23282860.20585864X-RAY DIFFRACTION100
1.43-1.450.2123370.18645842X-RAY DIFFRACTION100
1.45-1.470.18413090.16855852X-RAY DIFFRACTION99.84
1.47-1.50.18022940.16165853X-RAY DIFFRACTION99.18
1.5-1.520.16682910.14795914X-RAY DIFFRACTION100
1.52-1.540.16533230.13655869X-RAY DIFFRACTION99.98
1.54-1.570.16152900.1285894X-RAY DIFFRACTION100
1.57-1.60.1492800.12795920X-RAY DIFFRACTION100
1.6-1.630.14642960.12885902X-RAY DIFFRACTION99.98
1.63-1.660.14852960.12415900X-RAY DIFFRACTION100
1.66-1.70.15263100.12185898X-RAY DIFFRACTION100
1.7-1.740.14163140.12255929X-RAY DIFFRACTION99.89
1.74-1.780.1453060.1285847X-RAY DIFFRACTION99.27
1.78-1.830.14552840.11815927X-RAY DIFFRACTION100
1.83-1.890.12932870.11565944X-RAY DIFFRACTION100
1.89-1.950.1373260.11865920X-RAY DIFFRACTION100
1.95-2.020.1393270.12375907X-RAY DIFFRACTION99.97
2.02-2.10.15652860.1265965X-RAY DIFFRACTION100
2.1-2.190.153450.1315919X-RAY DIFFRACTION100
2.19-2.310.17353190.14265942X-RAY DIFFRACTION99.68
2.31-2.450.18633110.14935969X-RAY DIFFRACTION100
2.45-2.640.17013680.15095939X-RAY DIFFRACTION100
2.64-2.910.19093120.16596013X-RAY DIFFRACTION99.98
2.91-3.330.2022630.16786106X-RAY DIFFRACTION99.87
3.33-4.190.17193180.15126112X-RAY DIFFRACTION99.98
4.19-41.680.18952970.17326391X-RAY DIFFRACTION99.9

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