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- PDB-5zx3: Mycobacterium tuberculosis RNA polymerase holoenzyme with ECF sig... -

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Basic information

Entry
Database: PDB / ID: 5zx3
TitleMycobacterium tuberculosis RNA polymerase holoenzyme with ECF sigma factor sigma H
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • ECF RNA polymerase sigma factor SigH
KeywordsTRANSCRIPTION / Mycobacterium tuberculosis / RNA polymerase / holoenzyme / sigH
Function / homology
Function and homology information


response to nitrosative stress / 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 / : ...response to nitrosative stress / 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 / cellular response to heat / response to heat / response to oxidative stress / protein dimerization activity / response to antibiotic / 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 Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain ...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 Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / 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 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 / 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 Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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 / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.751 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)393,5938
Polymers393,4626
Non-polymers1312
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40250 Å2
ΔGint-189 kcal/mol
Surface area126630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.572, 159.790, 131.437
Angle α, β, γ (deg.)90.000, 118.720, 90.000
Int Tables number4
Space group name H-MP1211

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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 / 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: pETduet / 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 / 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: pACYCduet / 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' / 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: pACYCduet / 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 / 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: pETduet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WGY5, DNA-directed RNA polymerase

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Protein , 1 types, 1 molecules F

#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

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Non-polymers , 2 types, 55 molecules

#6: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.17 Å3/Da / Density % sol: 61.25 % / Description: rod
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M NaAc, 0.1 M sodium citrate pH5.5, 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97776 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 119837 / % possible obs: 98.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 78.9 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.036 / Rrim(I) all: 0.086 / Χ2: 1.065 / Net I/σ(I): 7 / Num. measured all: 650968
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.83.50.89351250.530.5151.0370.90284.3
2.8-2.854.10.83256100.6220.4480.950.91291.6
2.85-2.94.60.75858240.7070.3860.8540.93695.8
2.9-2.9650.64259590.7930.3140.7170.92898.1
2.96-3.035.10.54760140.8430.2630.610.93498.8
3.03-3.15.30.44259870.8970.210.4910.96798.7
3.1-3.175.90.3960720.9340.1750.4290.96999.8
3.17-3.265.90.30760790.9540.1380.338199.9
3.26-3.365.90.23860600.9680.1070.2621.03699.8
3.36-3.465.80.19160750.9790.0860.211.0799.8
3.46-3.595.70.1560900.9850.0680.1651.11199.8
3.59-3.735.50.11960580.990.0550.1311.17899.4
3.73-3.95.60.09660580.9920.0440.1061.20599.3
3.9-4.1160.0860920.9940.0360.0881.17499.8
4.11-4.365.90.0760910.9950.0310.0771.10199.8
4.36-4.75.80.0660950.9960.0270.0671.0899.9
4.7-5.175.50.05860990.9960.0270.0651.15799.5
5.17-5.9260.05661320.9960.0250.0621.0999.9
5.92-7.465.60.05161110.9960.0240.0571.18999.5
7.46-505.60.03962060.9980.0180.0441.14299.4

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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: 2.751→41.638 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2575 2159 1.8 %
Rwork0.2179 117484 -
obs0.2185 119643 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.46 Å2 / Biso mean: 90.5083 Å2 / Biso min: 36.94 Å2
Refinement stepCycle: final / Resolution: 2.751→41.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23256 0 2 53 23311
Biso mean--88.26 67.71 -
Num. residues----3063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323660
X-RAY DIFFRACTIONf_angle_d0.56532101
X-RAY DIFFRACTIONf_chiral_restr0.0443679
X-RAY DIFFRACTIONf_plane_restr0.0044256
X-RAY DIFFRACTIONf_dihedral_angle_d14.75914448
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7513-2.81530.27891080.29986499660781
2.8153-2.88570.40321400.31747429756994
2.8857-2.96370.33671340.31057842797698
2.9637-3.05090.35891470.29527869801699
3.0509-3.14930.30491580.287920807899
3.1493-3.26190.35351490.277280228171100
3.2619-3.39240.27111530.255279388091100
3.3924-3.54670.25491410.239880258166100
3.5467-3.73360.28021510.23457948809999
3.7336-3.96730.26441500.22357951810199
3.9673-4.27340.24281450.201579808125100
4.2734-4.70290.22211490.185980488197100
4.7029-5.38220.23151510.196679698120100
5.3822-6.77630.25761470.217380518198100
6.7763-41.64250.22221360.18117993812998

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