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- PDB-7u22: Mycobacterium tuberculosis RNA polymerase sigma A holoenzyme open... -

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Basic information

Entry
Database: PDB / ID: 7u22
TitleMycobacterium tuberculosis RNA polymerase sigma A holoenzyme open promoter complex containing UMN-7
Components
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • NT DNA
  • RNA polymerase sigma factor SigA
  • T DNA
KeywordsANTIBIOTIC / Transcription / inhibitor / rifabutin / transcription initiation / tuberculosis / MTB / Mycobacterium tuberculosis / Mycobacterium smegmatis
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
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 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, 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-KYO / DNA / DNA (> 10) / DNA-directed RNA polymerase subunit omega / RNA polymerase sigma factor SigA / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.87 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: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Redesign of Rifamycin Antibiotics to Overcome ADP-Ribosylation-Mediated Resistance.
Authors: Lan, T. / Ganapathy, U.S. / Sharma, S. / Ahn, Y.M. / Zimmerman, M. / Molodtsov, V. / Hegde, P. / Gengenbacher, M. / Ebright, R.H. / Dartois, V. / Freundlich, J.S. / Dick, T. / Aldrich, C.C.
History
DepositionFeb 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
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 SigA
G: T DNA
H: NT DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)435,37912
Polymers434,3078
Non-polymers1,0724
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48850 Å2
ΔGint-219 kcal/mol
Surface area138480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.482, 161.445, 196.603
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 6 and (name N or name...
d_2ens_1(chain "B" and (resid 6 through 157 or (resid 158...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGASNA4 - 224
d_21ens_1ARGASNB1 - 221

NCS oper: (Code: givenMatrix: (-0.847679819141, 0.306542001063, 0.432979128602), (0.450866500029, -0.0138208771231, 0.892484387823), (0.279568101494, 0.951756788754, -0.126493840511)Vector: 261. ...NCS oper: (Code: given
Matrix: (-0.847679819141, 0.306542001063, 0.432979128602), (0.450866500029, -0.0138208771231, 0.892484387823), (0.279568101494, 0.951756788754, -0.126493840511)
Vector: 261.849167847, 116.028935453, -229.846955798)

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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: Mycobacterium tuberculosis (bacteria) / 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: Mycobacterium tuberculosis (bacteria) / 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: Mycobacterium tuberculosis (bacteria)
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: Mycobacterium tuberculosis (bacteria)
References: UniProt: A0A045H2R3, DNA-directed RNA polymerase

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Protein , 1 types, 1 molecules F

#5: Protein RNA polymerase sigma factor SigA


Mass: 57877.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: sigA, hrdB_2, E5M05_04395, E5M52_03770, ERS007663_03246, ERS007679_00877, ERS007720_03380, ERS007722_02638, ERS013440_01579, ERS024276_00878, ERS027646_01351, ERS027661_00252, FPJ30_14815, ...Gene: sigA, hrdB_2, E5M05_04395, E5M52_03770, ERS007663_03246, ERS007679_00877, ERS007720_03380, ERS007722_02638, ERS013440_01579, ERS024276_00878, ERS027646_01351, ERS027661_00252, FPJ30_14815, FPJ31_14925, FPJ32_14805, FPJ33_14840, FPJ34_14810, FPJ35_14895, FPJ36_14815, FPJ37_14795, FPJ38_14835, FPJ39_14805, FPJ40_14780, FPJ41_14820, FPJ42_14710, FPJ43_14795, FPJ44_14890, FPJ45_14810, FPJ46_14810, FPJ47_14805, FPJ48_14815, FPJ49_14795, FPJ50_14780, FPJ51_14775, FPJ52_14815, FPJ53_14810, FPJ54_14810, FPJ55_14940, FPJ56_14795, FPJ57_14805, FPJ58_14795, FPJ59_14815, FPJ60_14800, FPJ61_14810, FPJ62_14770, FPJ63_14840, FPJ64_14895, FPJ65_14800, FPJ66_14800, FPJ67_14845, FPJ69_14845, FPJ70_14845, FPJ71_14840, FPJ72_13570, FPJ73_14770, FPJ76_14775, FPJ77_14810, FPJ78_14815, FPJ79_14755, FPJ80_14870, FPJ81_14945, FPJ82_15000, FPJ83_06790, FPJ84_14750, FPJ85_06790, FPJ86_06790, FPJ87_06790, FPJ88_14760, FPJ89_14830, FPJ90_14780, FPJ91_14825, FPJ92_14790, FPJ93_14765, FPJ94_13565, FPJ95_14765, FPJ96_14935, FPJ97_14820, FPJ98_14805, FPJ99_14805, FPK00_14720, FPK01_14735, FPK02_14730, FPK03_14735, FPK04_14750, FPK05_14830, FPK06_14715, FPK07_14740, FPK08_14915, FPK09_14905, FPK10_13550, FPK11_14770, FPK12_14740, FPK13_14815, FPK14_14750, FPK16_14740, FPK17_14835, FPK18_14780, FPK19_14825, FPK20_14820, FPK21_14790, FPK22_14780, HRD52_14230, HRD53_14220, SAMEA2683035_01696
Production host: Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HD00

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DNA chain , 2 types, 2 molecules GH

#6: DNA chain T DNA


Mass: 4939.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#7: DNA chain NT DNA


Mass: 7160.632 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)

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Non-polymers , 3 types, 4 molecules

#8: Chemical ChemComp-KYO / (9S,14S,15R,16S,17R,18R,19R,20S,21S,25R)-5,6,18,20-tetrahydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-(2-methylpropyl)-10,26-dioxo-1,3,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl benzoate


Mass: 917.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H72N4O11 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 20 mM Tris-HCl, pH 8.2, 200 mM potassium chloride, 20 mM magnesium chloride, 7% (m/v) PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.87→50 Å / Num. obs: 44566 / % possible obs: 98.96 % / Redundancy: 9.1 % / Biso Wilson estimate: 152.21 Å2 / CC1/2: 0.972 / Net I/σ(I): 9.04
Reflection shellResolution: 3.87→3.94 Å / Num. unique obs: 2282 / CC1/2: 0.38

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UHA

5uha


Resolution: 3.87→48.3 Å / SU ML: 0.5799 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.6731
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2781 1985 4.45 %
Rwork0.24 42581 -
obs0.2417 44566 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 187.97 Å2
Refinement stepCycle: LAST / Resolution: 3.87→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25200 656 69 0 25925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006626426
X-RAY DIFFRACTIONf_angle_d1.124835942
X-RAY DIFFRACTIONf_chiral_restr0.0434091
X-RAY DIFFRACTIONf_plane_restr0.0044621
X-RAY DIFFRACTIONf_dihedral_angle_d14.085410088
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.15346372185 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.87-3.970.37111240.33712887X-RAY DIFFRACTION95.38
3.97-4.070.38291500.30922949X-RAY DIFFRACTION97.79
4.07-4.190.33111390.28423000X-RAY DIFFRACTION98.93
4.19-4.330.33191420.26343025X-RAY DIFFRACTION99.59
4.33-4.480.33691260.24893035X-RAY DIFFRACTION98.9
4.48-4.660.24121570.23113021X-RAY DIFFRACTION99.87
4.66-4.880.29061400.21953026X-RAY DIFFRACTION99.72
4.88-5.130.29351450.21723047X-RAY DIFFRACTION99.75
5.13-5.450.25471450.22843042X-RAY DIFFRACTION99.81
5.45-5.870.30961440.25023052X-RAY DIFFRACTION99.35
5.87-6.460.31661350.25033103X-RAY DIFFRACTION99.91
6.46-7.40.31221470.26193086X-RAY DIFFRACTION99.85
7.4-9.310.23831460.21313127X-RAY DIFFRACTION99.7
9.31-48.30.23141450.22573181X-RAY DIFFRACTION97.02
Refinement TLS params.Method: refined / Origin x: 151.486304459 Å / Origin y: 170.334742801 Å / Origin z: 13.0158241558 Å
111213212223313233
T0.998618001407 Å2-0.00672040114473 Å20.0145498667702 Å2-1.05336979399 Å20.0381118517462 Å2--1.11450901953 Å2
L0.493212574376 °2-0.234021732605 °2-0.177449179134 °2-0.719543581308 °20.0865362589665 °2--0.773032583789 °2
S0.0170063614549 Å °0.0339406881048 Å °0.086411492111 Å °-0.162278057892 Å °-0.116834331482 Å °-0.0809640651452 Å °0.0460188982302 Å °0.0363907379496 Å °0.0880229857929 Å °
Refinement TLS groupSelection details: all

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