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- PDB-5zx2: Mycobacterium tuberculosis RNA polymerase transcription initiatio... -

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Basic information

Entry
Database: PDB / ID: 5zx2
TitleMycobacterium tuberculosis RNA polymerase transcription initiation complex with ECF sigma factor sigma H and 7nt RNA
Components
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • DNA (47-MER)
  • DNA (48-MER)
  • ECF RNA polymerase sigma factor SigH
  • RNA (5'-R(*CP*CP*CP*UP*CP*GP*A)-3')
KeywordsTRANSCRIPTION/DNA/RNA / Mycobacterium tuberculosis / RNA polymerase / sigma H / transcription initiation / TRANSCRIPTION-DNA-RNA complex
Function / homology
Function and homology information


response to nitrosative stress / Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / peptidoglycan-based cell wall / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cellular response to heat ...response to nitrosative stress / Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / peptidoglycan-based cell wall / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cellular response to heat / response to heat / response to oxidative stress / protein dimerization activity / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RNA polymerase sigma-70, actinobacteria / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase sigma-70 region 2 ...RNA polymerase sigma-70, actinobacteria / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / 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, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Beta Complex / 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 Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / 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, 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 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / ECF RNA polymerase sigma factor SigH / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLi, L. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670067 China
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for transcription initiation by bacterial ECF sigma factors.
Authors: Li, L. / Fang, C. / Zhuang, N. / Wang, T. / Zhang, Y.
History
DepositionMay 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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
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: ECF RNA polymerase sigma factor SigH
G: DNA (48-MER)
H: DNA (47-MER)
I: RNA (5'-R(*CP*CP*CP*UP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)425,17311
Polymers425,0429
Non-polymers1312
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56430 Å2
ΔGint-261 kcal/mol
Surface area133460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.824, 164.027, 214.792
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 40279.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: rpoA, Rv3457c, MTCY13E12.10c / Plasmid: pACYCduet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WGZ1, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 129602.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: rpoB, Rv0667, MTCI376.08c / Plasmid: pETduet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WGY9, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / Polymerase / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 147068.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: rpoC, Rv0668, MTCI376.07c / Plasmid: pETduet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WGY7, 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 H37Rv (bacteria)
Strain: H37Rv / Gene: rpoZ, Rv1390, MTCY21B4.07 / Plasmid: pACYCduet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WGY5, DNA-directed RNA polymerase

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DNA chain , 2 types, 2 molecules GH

#6: DNA chain DNA (48-MER)


Mass: 14847.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (47-MER)


Mass: 14576.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / RNA chain , 2 types, 2 molecules FI

#5: Protein ECF RNA polymerase sigma factor SigH / ECF sigma factor SigH / Alternative RNA polymerase sigma factor SigH / RNA polymerase sigma-H ...ECF sigma factor SigH / Alternative RNA polymerase sigma factor SigH / RNA polymerase sigma-H factor / Sigma-H factor


Mass: 24382.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: sigH, rpoE, Rv3223c, MTCY07D11.03 / Plasmid: pTOLO-EX5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WGH9
#8: RNA chain RNA (5'-R(*CP*CP*CP*UP*CP*GP*A)-3')


Mass: 2156.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 49 molecules

#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 2% Tacsimate pH 5.0, 0.1 M Sodium citrate pH5.6, 16 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 113375 / % possible obs: 99.8 % / Redundancy: 8.5 % / Biso Wilson estimate: 60.59 Å2 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.059 / Rrim(I) all: 0.175 / Χ2: 1.106 / Net I/σ(I): 6.9 / Num. measured all: 963049
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.858.41.4355640.5470.5181.5240.8799.5
2.85-2.98.61.24156000.6390.4471.3220.87699.8
2.9-2.968.81.1156420.6910.3981.180.899100
2.96-3.028.80.94256100.7680.3371.0010.913100
3.02-3.088.70.79856110.8140.2870.8490.932100
3.08-3.158.60.66956350.8520.2420.7120.94599.9
3.15-3.238.50.54956210.8830.2010.5850.993100
3.23-3.328.40.43356270.9310.1590.4621.02999.9
3.32-3.427.90.34856630.9430.1320.3731.08499.8
3.42-3.537.80.27355980.9640.1030.2931.16699.5
3.53-3.6590.24156550.9770.0850.2561.213100
3.65-3.890.19256600.9850.0670.2031.237100
3.8-3.978.90.16256470.9890.0570.1721.17100
3.97-4.188.70.13256790.9910.0470.1411.249100
4.18-4.448.60.11556910.9930.0410.1221.277100
4.44-4.798.30.156860.9940.0360.1061.28399.7
4.79-5.277.60.09456910.9940.0350.1011.20599.4
5.27-6.038.90.09257450.9950.0320.0971.295100
6.03-7.598.60.07558090.9970.0270.081.27399.9
7.59-507.60.05359410.9970.020.0571.19998.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000v716data scaling
PDB_EXTRACT3.24data extraction
HKL-2000v716data reduction
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TW1

5tw1


Resolution: 2.8→36.941 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 2283 2.02 %
Rwork0.22 110686 -
obs0.2207 112969 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.22 Å2 / Biso mean: 66.0881 Å2 / Biso min: 23.34 Å2
Refinement stepCycle: final / Resolution: 2.8→36.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23744 2065 2 47 25858
Biso mean--69.22 43 -
Num. residues----3199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00526477
X-RAY DIFFRACTIONf_angle_d0.62136330
X-RAY DIFFRACTIONf_chiral_restr0.0444154
X-RAY DIFFRACTIONf_plane_restr0.0044428
X-RAY DIFFRACTIONf_dihedral_angle_d18.18315793
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.86090.38011410.340368236964100
2.8609-2.92740.3671420.326268546996100
2.9274-3.00060.3411410.314568586999100
3.0006-3.08170.31641420.30868426984100
3.0817-3.17230.33671410.301268917032100
3.1723-3.27460.3091420.288568526994100
3.2746-3.39160.32851400.263768607000100
3.3916-3.52730.27051430.242868697012100
3.5273-3.68770.29041410.230868807021100
3.6877-3.88190.2731430.222769327075100
3.8819-4.12480.2541440.199269227066100
4.1248-4.44280.24981420.183269297071100
4.4428-4.8890.22511440.174869477091100
4.889-5.59430.23561430.195569577100100
5.5943-7.04030.2151460.208670527198100
7.0403-36.9440.17221480.17267218736699

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