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- PDB-6tye: Crystal structure of MTB sigma L transcription initiation complex... -

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Basic information

Entry
Database: PDB / ID: 6tye
TitleCrystal structure of MTB sigma L transcription initiation complex with 5 nt long RNA primer
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • DNA (5'-D(*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*AP*TP*CP*GP*AP*GP*G)-3')
  • DNA (5'-D(P*GP*TP*GP*TP*CP*AP*GP*TP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*C)-3')
  • RNA (5'-R(P*CP*UP*CP*GP*A)-3')
  • RNA polymerase sigma factor
KeywordsTRANSCRIPTION / tuberculosis / initiation / sigma finger displacement
Function / homology
Function and homology information


Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity ...Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 ...RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / 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 / Gyrase A; domain 2 / 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 beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / Beta Complex / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / 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 / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / RNA polymerase, RBP11-like subunit / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase subunit omega / RNA polymerase sigma factor / : / DNA-directed RNA polymerase subunit alpha / ECF RNA polymerase sigma factor SigL / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' ...DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase subunit omega / RNA polymerase sigma factor / : / DNA-directed RNA polymerase subunit alpha / ECF RNA polymerase sigma factor SigL / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.79 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
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Authors: Li, L. / Molodtsov, V. / Lin, W. / Ebright, R.H. / Zhang, Y.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionAug 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: RNA polymerase sigma factor
G: DNA (5'-D(*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*AP*TP*CP*GP*AP*GP*G)-3')
H: DNA (5'-D(P*GP*TP*GP*TP*CP*AP*GP*TP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*C)-3')
I: RNA (5'-R(P*CP*UP*CP*GP*A)-3')
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


Theoretical massNumber of molelcules
Total (without water)399,0649
Polymers399,0649
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49000 Å2
ΔGint-221 kcal/mol
Surface area128320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.527, 158.522, 214.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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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DNA chain , 2 types, 2 molecules GH

#2: DNA chain DNA (5'-D(*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*AP*TP*CP*GP*AP*GP*G)-3')


Mass: 5252.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#3: DNA chain DNA (5'-D(P*GP*TP*GP*TP*CP*AP*GP*TP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*C)-3')


Mass: 8373.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)

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

#5: Protein DNA-directed RNA polymerase subunit alpha / 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, UniProt: P9WGZ1*PLUS, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerase subunit beta / 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, UniProt: P9WGY9*PLUS, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase subunit beta' / 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, ERS027656_00588 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0E8TXU5, UniProt: P9WGY7*PLUS, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase subunit omega / 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, UniProt: P9WGY5*PLUS, DNA-directed RNA polymerase

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Protein / RNA chain , 2 types, 2 molecules FI

#1: 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, UniProt: P9WGH5*PLUS
#4: RNA chain RNA (5'-R(P*CP*UP*CP*GP*A)-3')


Mass: 1545.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)

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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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate tribasic dihydrate, pH 5.6, 200 mM sodium acetate, and 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: Jul 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.79→48.02 Å / Num. obs: 42832 / % possible obs: 99 % / Redundancy: 9 % / Biso Wilson estimate: 60.21 Å2 / CC1/2: 0.879 / Net I/σ(I): 9.1
Reflection shellResolution: 3.83→3.94 Å / Num. unique obs: 3288 / CC1/2: 0.879

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DVC

6dvc


Resolution: 3.79→48.016 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 1904 4.45 %
Rwork0.2348 --
obs0.2367 42832 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.79→48.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23850 929 0 0 24779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00325296
X-RAY DIFFRACTIONf_angle_d0.63334478
X-RAY DIFFRACTIONf_dihedral_angle_d9.32315312
X-RAY DIFFRACTIONf_chiral_restr0.0433937
X-RAY DIFFRACTIONf_plane_restr0.0044388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.79-3.88470.35761020.30332197X-RAY DIFFRACTION74
3.8847-3.98970.3441150.28552481X-RAY DIFFRACTION83
3.9897-4.10710.31961280.24972771X-RAY DIFFRACTION92
4.1071-4.23960.28431380.24532936X-RAY DIFFRACTION98
4.2396-4.3910.29641380.24182998X-RAY DIFFRACTION100
4.391-4.56670.2721410.22593024X-RAY DIFFRACTION100
4.5667-4.77430.27691410.22613029X-RAY DIFFRACTION100
4.7743-5.02580.26951400.2253011X-RAY DIFFRACTION100
5.0258-5.34030.25211420.23113021X-RAY DIFFRACTION100
5.3403-5.7520.26571390.23543030X-RAY DIFFRACTION100
5.752-6.32970.28441430.23913060X-RAY DIFFRACTION100
6.3297-7.24290.26041430.24573073X-RAY DIFFRACTION100
7.2429-9.11510.22761450.19843099X-RAY DIFFRACTION100
9.1151-48.0160.2771490.21613198X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 3.1559 Å / Origin y: -7.7327 Å / Origin z: -15.4971 Å
111213212223313233
T0.3416 Å2-0.0329 Å2-0.035 Å2-0.2859 Å20.0432 Å2--0.3216 Å2
L0.5899 °20.158 °20.1872 °2-0.8359 °2-0.0189 °2--0.9696 °2
S0.0391 Å °-0.0539 Å °-0.0507 Å °-0.1554 Å °-0.1598 Å °0.0584 Å °-0.0713 Å °-0.0315 Å °0.0938 Å °
Refinement TLS groupSelection details: all

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