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

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Basic information

Entry
Database: PDB / ID: 8cwr
TitleComplex structure of WhiB3 and the SigmaAr4-RNAP Beta flap tip chimera in space group R3
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.2Oct 25, 2023Group: 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: Redox- and pH-responsive transcriptional regulator WhiB3
B: RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7619
Polymers22,9192
Non-polymers8427
Water1,892105
1
A: Redox- and pH-responsive transcriptional regulator WhiB3
B: RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta
hetero molecules

A: Redox- and pH-responsive transcriptional regulator WhiB3
B: RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta
hetero molecules

A: Redox- and pH-responsive transcriptional regulator WhiB3
B: RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,28327
Polymers68,7576
Non-polymers2,52621
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17350 Å2
ΔGint-319 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.809, 120.809, 31.758
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11B-601-

SO4

21B-601-

SO4

31B-605-

NI

41B-762-

HOH

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 10268.640 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first five residues are not observed in the final structure
Source: (gene. exp.) Mycobacterium tuberculosis (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


Mass: 12650.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The 82 residues in the C-terminal of RNA polymerase 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 (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, 112 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.96 Å3/Da / Density % sol: 37.4 % / Description: Tiny triangle-shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion / 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: Collect 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: Feb 11, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 27421 / % possible obs: 99.8 % / Redundancy: 18.1 % / Biso Wilson estimate: 26.01 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.018 / Rrim(I) all: 0.079 / Χ2: 1.092 / Net I/σ(I): 45.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 14.2 % / Rmerge(I) obs: 2.16 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2696 / CC1/2: 0.713 / CC star: 0.922 / Rpim(I) all: 0.578 / Rrim(I) all: 2.239 / Χ2: 0.575 / % possible all: 99.7

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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: MOLECULAR REPLACEMENT
Starting model: 8CWT

8cwt


Resolution: 1.5→34.87 Å / SU ML: 0.2003 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.139
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Refined with Phenix.refine GUI. Both B-factors and individual B-factors are refined.
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 1312 4.78 %Random selection
Rwork0.1828 26109 --
obs0.1843 27421 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.31 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 0 29 105 1675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111614
X-RAY DIFFRACTIONf_angle_d1.28952185
X-RAY DIFFRACTIONf_chiral_restr0.0741229
X-RAY DIFFRACTIONf_plane_restr0.0088287
X-RAY DIFFRACTIONf_dihedral_angle_d29.5233616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.560.36981370.30632888X-RAY DIFFRACTION98.86
1.56-1.630.28521630.2562877X-RAY DIFFRACTION99.8
1.63-1.720.23291660.22472876X-RAY DIFFRACTION99.87
1.72-1.830.26621020.20632954X-RAY DIFFRACTION99.71
1.83-1.970.24991460.19862919X-RAY DIFFRACTION99.74
1.97-2.170.19791490.18262880X-RAY DIFFRACTION99.9
2.17-2.480.20381600.18092902X-RAY DIFFRACTION99.8
2.48-3.130.21481360.19862920X-RAY DIFFRACTION99.87
3.13-34.870.19771530.16062893X-RAY DIFFRACTION99.71
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.725040575771.02909620582-0.1718301526047.11572604225-0.1344394594584.614810626980.0516628845977-0.2019667236220.3344065617680.0645028684854-0.2016714403810.875304439644-0.20324807037-0.3503350584740.004530291906080.269596813962-0.033855208604-0.03317378459210.382808284827-0.08741609308530.377022678294-31.7699505699-14.71954165225.03040149147
21.2975713821.09992912344-0.2352404581841.86112989364-0.02375010299311.24386746340.01967975060920.0376189248338-0.02007150779110.1361543353020.01849494144310.06524709517360.196763508928-0.148360196858-0.03343990136810.206595633249-0.0139428158844-0.002887513691940.211197201398-0.01383905053370.152672136863-13.9619884505-9.4648204011214.449573594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 90)
2X-RAY DIFFRACTION2(chain 'B' and resid 439 through 547)

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