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- PDB-8cyf: WhiB3 bound to SigmaAr4-RNAP Beta flap tip chimera and DNA -

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Basic information

Entry
Database: PDB / ID: 8cyf
TitleWhiB3 bound to SigmaAr4-RNAP Beta flap tip chimera and DNA
Components
  • DNA (5'-D(*CP*AP*CP*CP*AP*CP*AP*AP*CP*CP*GP*AP*TP*TP*TP*T)-3')
  • DNA (5'-D(*GP*AP*AP*AP*AP*TP*CP*GP*GP*TP*TP*GP*TP*GP*GP*T)-3')
  • RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera,DNA-directed RNA polymerase subunit beta
  • Redox- and pH-responsive transcriptional regulator WhiB3
KeywordsTRANSCRIPTION/DNA/Transferase / redox sensor / transcriptional factor / protein-DNA complex / TRANSCRIPTION / TRANSCRIPTION-DNA-Transferase complex
Function / homology
Function and homology information


response to host redox environment / Actinobacterium-type cell wall biogenesis / dinitrosyl-iron complex binding / protein-disulfide reductase [NAD(P)H] activity / sigma factor activity / iron-sulfur cluster binding / regulation of lipid metabolic process / protein-disulfide reductase activity / DNA-directed RNA polymerase complex / cell redox homeostasis ...response to host redox environment / Actinobacterium-type cell wall biogenesis / dinitrosyl-iron complex binding / protein-disulfide reductase [NAD(P)H] activity / sigma factor activity / iron-sulfur cluster binding / 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 / 4 iron, 4 sulfur cluster binding / negative regulation of DNA-templated transcription / DNA binding / metal ion binding / cytoplasm
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 / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
CACODYLATE ION / IRON/SULFUR CLUSTER / DNA / DNA (> 10) / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit beta / Redox- and pH-responsive transcriptional regulator WhiB3
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsWan, T. / Zhang, L.M.
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 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jun 14, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 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, DNA-directed RNA polymerase subunit beta chimera,DNA-directed RNA polymerase subunit beta
C: DNA (5'-D(*GP*AP*AP*AP*AP*TP*CP*GP*GP*TP*TP*GP*TP*GP*GP*T)-3')
D: DNA (5'-D(*CP*AP*CP*CP*AP*CP*AP*AP*CP*CP*GP*AP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5656
Polymers34,0764
Non-polymers4892
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.697, 72.934, 95.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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

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Protein , 2 types, 2 molecules AB

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


Mass: 11630.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Full WhiB3 sequence was used for crystallization, the N- and C- terminal residues are not visible due to flexibility.
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, DNA-directed RNA polymerase subunit beta chimera,DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 12650.234 Da / Num. of mol.: 1
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 in the N- ...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 in the N-terminal,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 in the N-terminal
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: sigA, ERS007670_01286, ERS007681_03833, ERS007688_01862
Production host: Escherichia coli (E. coli)
References: UniProt: A0A654TMB9, UniProt: A1KGE7, DNA-directed RNA polymerase

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain DNA (5'-D(*GP*AP*AP*AP*AP*TP*CP*GP*GP*TP*TP*GP*TP*GP*GP*T)-3')


Mass: 4993.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA sequence from WhiB7 promoter / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#4: DNA chain DNA (5'-D(*CP*AP*CP*CP*AP*CP*AP*AP*CP*CP*GP*AP*TP*TP*TP*T)-3')


Mass: 4802.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA sequence from WhiB7 promoter / Source: (synth.) Mycobacterium tuberculosis (bacteria)

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Non-polymers , 3 types, 5 molecules

#5: 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
#6: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.59 Å3/Da / Density % sol: 52.6 % / Description: Large diamond-shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Ca(Ac)2, 0.1 M Na Cacodylate, pH 6.5, 10%~13% PEG8000
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: 0.9787 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 13547 / % possible obs: 99.4 % / Redundancy: 15.3 % / Biso Wilson estimate: 66.33 Å2 / CC1/2: 0.987 / CC star: 0.994 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.034 / Rrim(I) all: 0.132 / Χ2: 0.886 / Net I/σ(I): 25.4
Reflection shellResolution: 2.44→2.49 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.344 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 617 / CC1/2: 0.713 / CC star: 0.912 / Rpim(I) all: 1.441 / Rrim(I) all: 0.508 / Χ2: 0.469 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHASER1.20.1_4487phasing
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8CWR

8cwr


Resolution: 2.44→38.15 Å / SU ML: 0.3954 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.0463
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2513 673 4.99 %
Rwork0.2224 12803 -
obs0.2238 13476 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.27 Å2
Refinement stepCycle: LAST / Resolution: 2.44→38.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 650 13 3 1974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01752069
X-RAY DIFFRACTIONf_angle_d2.22752924
X-RAY DIFFRACTIONf_chiral_restr0.2125321
X-RAY DIFFRACTIONf_plane_restr0.0115268
X-RAY DIFFRACTIONf_dihedral_angle_d27.0476833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.630.42561170.3852431X-RAY DIFFRACTION95.83
2.63-2.90.30251550.27982514X-RAY DIFFRACTION99.55
2.9-3.320.28631420.26722556X-RAY DIFFRACTION99.85
3.32-4.180.23841190.2152607X-RAY DIFFRACTION99.85
4.18-38.150.22331400.1912695X-RAY DIFFRACTION99.06
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)
17.974380955951.875456873170.9637620231826.435561720480.4683826857656.198520405430.181949957002-0.556749091043-0.1531440423120.265735636789-0.2042414688620.2969854822650.0267046305833-0.285302907206-0.01000172469870.4404496464560.02567030302050.03931950164260.352726575660.02763993166560.43845158566216.130252032225.06497907828.9010176596
24.076659929781.495600376010.3967578324495.274973716670.02696496918482.756472323890.1322512003530.002713408451390.8155303743570.001528095284030.1045034569020.856280398198-0.448633428204-0.595501918958-0.1859191650470.5523687609380.1190610289980.06472505104480.5034385881020.09965858759780.64835360716117.218404645742.781112180218.2608430092
31.6161318604-1.54880528896-0.4518664017953.86367944195-2.236648997853.09438041880.269075801098-0.156694507867-0.3211618354250.270650728908-0.235937495063-0.0928420487576-0.404796934353-0.734255135604-0.05043991692320.588535836714-0.0670892058836-0.1170621272270.7836515768930.02965226868520.61276649102540.168035327731.222454530833.4165909368
41.95429570801-1.202524498241.708578263795.079819490610.5728989540053.971705828510.172281669155-0.520482504575-0.3746791570530.8546012436320.344212390642-0.2226382190460.2642178232090.926767785134-0.5401118093610.636766921976-0.00111063534083-0.09500385368021.040910933030.02531697918270.67217307221341.479962396234.259183442635.3906567184
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 16 through 90)AA16 - 901 - 75
22(chain 'B' and resid 450 through 546)BC450 - 5461 - 89
33(chain 'C' and resid 1 through 16)CE1 - 16
44(chain 'D' and resid 1 through 16)DF1 - 16

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