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- PDB-7rwi: Mycobacterium tuberculosis RNA polymerase sigma L holoenzyme open... -

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Basic information

Entry
Database: PDB / ID: 7rwi
TitleMycobacterium tuberculosis RNA polymerase sigma L holoenzyme open promoter complex containing TNP-2198
Components
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • NT DNA
  • RNA polymerase sigma factor
  • T DNA
KeywordsTRANSCRIPTION/INHIBITOR / Mycobacterium tuberculosis / RNA polymerase / transcription inhibitor / TNP-2198 / open promoter complex / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription / magnesium ion binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / 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 ...RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / 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, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / 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 / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like 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
Chem-7US / DNA / DNA (> 10) / DNA-directed RNA polymerase subunit omega / RNA polymerase sigma factor / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsMolodtsov, V. / Ebright, R.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: Design, Synthesis, and Characterization of TNP-2198, a Dual-Targeted Rifamycin-Nitroimidazole Conjugate with Potent Activity against Microaerophilic and Anaerobic Bacterial Pathogens.
Authors: Ma, Z. / He, S. / Yuan, Y. / Zhuang, Z. / Liu, Y. / Wang, H. / Chen, J. / Xu, X. / Ding, C. / Molodtsov, V. / Lin, W. / Robertson, G.T. / Weiss, W.J. / Pulse, M. / Nguyen, P. / Duncan, L. / ...Authors: Ma, Z. / He, S. / Yuan, Y. / Zhuang, Z. / Liu, Y. / Wang, H. / Chen, J. / Xu, X. / Ding, C. / Molodtsov, V. / Lin, W. / Robertson, G.T. / Weiss, W.J. / Pulse, M. / Nguyen, P. / Duncan, L. / Doyle, T. / Ebright, R.H. / Lynch, A.S.
History
DepositionAug 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor
G: T DNA
H: NT DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)400,3309
Polymers399,3808
Non-polymers9501
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.773, 160.613, 238.646
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 5 or (resid 6...
d_2ens_1(chain "B" and resid 2 through 226)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUASNA1 - 225
d_21ens_1LEUASNB2 - 226

NCS oper: (Code: givenMatrix: (-0.881237687082, -0.239462391804, 0.407526565734), (-0.425011018795, 0.0241315914238, -0.904866454345), (0.206847220842, -0.970605702233, -0.123039822915)Vector: -46. ...NCS oper: (Code: given
Matrix: (-0.881237687082, -0.239462391804, 0.407526565734), (-0.425011018795, 0.0241315914238, -0.904866454345), (0.206847220842, -0.970605702233, -0.123039822915)
Vector: -46.3664855685, -2.47706231436, 13.1864265985)

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Components

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE

#1: Protein DNA-directed RNA polymerase subunit alpha / Polymerase / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 37745.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: rpoA / Production host: Escherichia coli (E. coli) / References: UniProt: A5U8D3, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 130018.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: rpoB / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGY8, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / Polymerase / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 146968.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: rpoC, rpoC_1, rpoC_2, DKC2_0716, ERS007665_00591, ERS023446_00410, ERS031537_00289, ERS124361_01694, EUB02_01475, EUB03_00860, EUB11_05575, SAMEA2682835_07420, SAMEA2682864_01702
Production host: Escherichia coli (E. coli)
References: UniProt: A0A045J9E2, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / Polymerase / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 11851.140 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: rpoZ, DKC2_1480, DSI35_24025, ERS007657_03145, ERS007661_02963, ERS007663_02972, ERS007665_03743, ERS007670_03615, ERS007679_02942, ERS007681_04445, ERS007722_03066, ERS007741_03196, ERS023446_ ...Gene: rpoZ, DKC2_1480, DSI35_24025, ERS007657_03145, ERS007661_02963, ERS007663_02972, ERS007665_03743, ERS007670_03615, ERS007679_02942, ERS007681_04445, ERS007722_03066, ERS007741_03196, ERS023446_03677, ERS024213_01369, ERS024276_01577, ERS027644_00478, ERS027646_01439, ERS027651_03169, ERS027653_00843, ERS027659_01429, ERS027661_02200, ERS027666_04715, ERS031537_03443, EU767_08910, EU768_15085, EU769_05250, EU770_14555, EU771_05130, EU773_14340, EU774_06465, EU775_07590, EU776_17830, EU777_06800, EUB02_12495, EUB03_09550, EUB06_03645, EUB07_12165, EUB08_05285, EUB09_00425, EUB10_04215, EUB11_10790, EUB13_01060, EUB14_01055, EUB16_00425, SAMEA2682864_01599, SAMEA2683035_01133
Production host: Escherichia coli (E. coli)
References: UniProt: A0A045H2R3, DNA-directed RNA polymerase

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DNA chain , 2 types, 2 molecules GH

#6: DNA chain T DNA


Mass: 7113.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain NT DNA


Mass: 8373.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / Non-polymers , 2 types, 2 molecules F

#5: Protein RNA polymerase sigma factor


Mass: 19563.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: sigL, sigX, DKC2_0784, DSI35_13315, ERS007657_01744, ERS007661_01946, ERS007670_03245, ERS007672_04865, ERS007688_03724, ERS007722_03570, ERS007731_02151, ERS007741_04102, ERS023446_03871, ...Gene: sigL, sigX, DKC2_0784, DSI35_13315, ERS007657_01744, ERS007661_01946, ERS007670_03245, ERS007672_04865, ERS007688_03724, ERS007722_03570, ERS007731_02151, ERS007741_04102, ERS023446_03871, ERS024213_03781, ERS027644_01708, ERS027646_03649, ERS027651_00554, ERS027654_02031, ERS027659_03608, ERS027661_02428, ERS027666_03497, ERS031537_01383, ERS124361_02832, EU767_20440, EU768_17405, EU769_19535, EU770_10565, EU771_18640, EU773_15915, EU774_01235, EU775_01235, EU776_08285, EU777_18775, EUB02_13395, EUB03_01225, EUB07_01225, EUB08_01615, EUB09_12390, EUB10_16580, EUB11_05940, EUB12_18145, EUB13_14065, EUB14_03980, EUB16_03020, SAMEA2682835_06130, SAMEA2682864_01771, SAMEA2683035_02456
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045IR27
#8: Chemical ChemComp-7US / (3aM,9S,10bP,14S,15R,16S,17R,18R,19R,20S,21S,25R)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate


Mass: 950.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H67N7O13

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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: 3.43 Å3/Da / Density % sol: 64.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate tribasic dihydrate, pH 5.6, 200 mM sodium acetate, 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.7→48.71 Å / Num. obs: 57449 / % possible obs: 97.3 % / Redundancy: 13.5 % / Biso Wilson estimate: 132.07 Å2 / CC1/2: 0.997 / Net I/σ(I): 2.3
Reflection shellResolution: 3.7→3.76 Å / Num. unique obs: 5560 / CC1/2: 0.787 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6DVE

6dve


Resolution: 3.7→48.71 Å / SU ML: 0.4277 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0015
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2451 1997 3.48 %
Rwork0.208 55365 -
obs0.2093 57362 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 167.57 Å2
Refinement stepCycle: LAST / Resolution: 3.7→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24038 797 68 0 24903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004425416
X-RAY DIFFRACTIONf_angle_d0.621734628
X-RAY DIFFRACTIONf_chiral_restr0.05953944
X-RAY DIFFRACTIONf_plane_restr0.00534423
X-RAY DIFFRACTIONf_dihedral_angle_d13.21979660
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.29229098934 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.80.3311390.29763875X-RAY DIFFRACTION96.58
3.8-3.90.33111430.27583997X-RAY DIFFRACTION99
3.9-4.010.27531440.24983974X-RAY DIFFRACTION98.82
4.01-4.140.2481440.22983972X-RAY DIFFRACTION99.06
4.14-4.290.2521420.19753958X-RAY DIFFRACTION97.97
4.29-4.460.2571320.19173658X-RAY DIFFRACTION90.35
4.46-4.660.22181430.17533972X-RAY DIFFRACTION98.37
4.66-4.910.22511450.18384010X-RAY DIFFRACTION99.28
4.91-5.220.24771460.1964034X-RAY DIFFRACTION99.43
5.22-5.620.24931430.19633972X-RAY DIFFRACTION97.72
5.62-6.180.2531380.21463826X-RAY DIFFRACTION93.12
6.19-7.080.23511480.21214072X-RAY DIFFRACTION99.6
7.08-8.910.21311410.20353922X-RAY DIFFRACTION94.01
8.91-48.710.24371490.20354123X-RAY DIFFRACTION95.81
Refinement TLS params.Method: refined / Origin x: -6.65478663537 Å / Origin y: 1.75374614162 Å / Origin z: -21.7081076955 Å
111213212223313233
T0.96222162816 Å20.0594385956809 Å2-0.033774459567 Å2-0.825456148496 Å20.0500406082096 Å2--0.805973208222 Å2
L0.674807520575 °20.155372299149 °2-0.225721252958 °2-0.456109405523 °2-0.189523786092 °2--0.515298410905 °2
S0.0205563122524 Å °0.103854997012 Å °0.175529016035 Å °-0.103727530441 Å °-0.0702534718948 Å °0.00250052174197 Å °-0.31998593602 Å °0.0408340051633 Å °0.0378602819186 Å °
Refinement TLS groupSelection details: all

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