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- PDB-4zh3: Crystal structure of Escherichia coli RNA polymerase in complex w... -

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Basic information

Entry
Database: PDB / ID: 4zh3
TitleCrystal structure of Escherichia coli RNA polymerase in complex with CBRH16-Br
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA polymerase sigma factor RpoD
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / RNA polymerase / inhibitor / transcription / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility ...sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation / regulation of DNA-templated transcription elongation / transcription elongation factor complex / transcription antitermination / cell motility / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / 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 ...RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / 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 beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / 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
Similarity search - Domain/homology
Chem-4OD / RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.082 Å
AuthorsFeng, Y. / Ebright, R.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM041376 United States
CitationJournal: Structure / Year: 2015
Title: Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles.
Authors: Feng, Y. / Degen, D. / Wang, X. / Gigliotti, M. / Liu, S. / Zhang, Y. / Das, D. / Michalchuk, T. / Ebright, Y.W. / Talaue, M. / Connell, N. / Ebright, R.H.
History
DepositionApr 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: RNA polymerase sigma factor RpoD
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)924,19420
Polymers923,12912
Non-polymers1,0658
Water00
1
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 RpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)462,09710
Polymers461,5656
Non-polymers5324
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38710 Å2
ΔGint-178 kcal/mol
Surface area160900 Å2
MethodPISA
2
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)462,09710
Polymers461,5656
Non-polymers5324
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38030 Å2
ΔGint-180 kcal/mol
Surface area162670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.339, 205.790, 307.630
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, 10 molecules ABGHCIDJEK

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


Mass: 37387.547 Da / Num. of mol.: 4 / Fragment: N-terminal domain (UNP residues 1-234)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 150820.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12
Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
Production host: Escherichia coli (E. coli) / References: UniProt: P0A8V2, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 155366.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rpoC, tabB, b3988, JW3951 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8T7, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 10249.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rpoZ, b3649, JW3624 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A800, DNA-directed RNA polymerase

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Protein , 1 types, 2 molecules FL

#5: Protein RNA polymerase sigma factor RpoD / Sigma-70


Mass: 70352.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rpoD, alt, b3067, JW3039 / Production host: Escherichia coli (E. coli) / References: UniProt: P00579

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Non-polymers , 3 types, 8 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-4OD / N'-(3-bromophenyl)-4-fluoro-N-hydroxy-3-(trifluoromethyl)benzenecarboximidamide


Mass: 377.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H9BrF4N2O

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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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 0.2 M calcium chloride, 18% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 4.1→50 Å / Num. obs: 94040 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 141.76 Å2 / Rmerge(I) obs: 0.234 / Rpim(I) all: 0.068 / Rrim(I) all: 0.244 / Χ2: 1.005 / Net I/av σ(I): 10.145 / Net I/σ(I): 7 / Num. measured all: 1244252
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2
4.1-4.1713.20.76146500.9110.2170.7920.993
4.17-4.2513.30.66446590.9330.1890.691.004
4.25-4.3313.30.57546300.9460.1630.5980.992
4.33-4.4213.30.52646480.9480.1490.5471.002
4.42-4.5113.30.46646520.9580.1320.4850.992
4.51-4.6213.30.40946520.9610.1160.4260.991
4.62-4.7313.40.38146480.9670.1080.3960.996
4.73-4.8613.30.34946480.9690.0990.3630.981
4.86-513.40.33746860.9610.0960.3510.978
5-5.1613.40.32746850.9680.0930.3410.977
5.16-5.3513.40.30746540.9730.0870.3190.966
5.35-5.5613.40.29446890.9720.0840.3060.955
5.56-5.8213.40.27446920.9750.0780.2850.953
5.82-6.1213.40.25646860.9720.0730.2660.935
6.12-6.513.40.22947220.9760.0650.2380.937
6.5-7.0113.30.2147040.9770.060.2190.966
7.01-7.7113.20.1947480.9760.0540.1980.991
7.71-8.8213.10.1847710.980.0520.1881.018
8.82-11.0912.70.17847960.9770.0520.1851.053
11.09-5012.40.20950200.9390.0620.2181.424

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4LK1

4lk1


Resolution: 4.082→49.751 Å / FOM work R set: 0.794 / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2669 3348 1.98 %
Rwork0.2375 165775 -
obs0.2381 91294 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 400.81 Å2 / Biso mean: 114.89 Å2 / Biso min: 0.12 Å2
Refinement stepCycle: final / Resolution: 4.082→49.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms57487 0 50 0 57537
Biso mean--91.93 --
Num. residues----7357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00558358
X-RAY DIFFRACTIONf_angle_d0.97878794
X-RAY DIFFRACTIONf_chiral_restr0.0649006
X-RAY DIFFRACTIONf_plane_restr0.00510333
X-RAY DIFFRACTIONf_dihedral_angle_d16.57422415
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.0825-4.14080.31841130.31135574568775
4.1408-4.20250.32271260.28446351647786
4.2025-4.26820.24171270.28166442656987
4.2682-4.33810.30741380.27396469660787
4.3381-4.41290.30411280.27596573670188
4.4129-4.49310.3221230.26546581670489
4.4931-4.57940.28011330.25376756688991
4.5794-4.67280.30621380.25266793693191
4.6728-4.77440.26481430.24526829697292
4.7744-4.88530.27451410.23886874701593
4.8853-5.00740.26731360.23936923705993
5.0074-5.14260.29321420.25117004714694
5.1426-5.29380.28971420.24657015715795
5.2938-5.46450.29361440.24257069721395
5.4645-5.65950.27241390.24397107724696
5.6595-5.88580.31481430.24997128727196
5.8858-6.15320.28811470.25337144729197
6.1532-6.47690.3081500.23667221737197
6.4769-6.88180.2971460.23657295744198
6.8818-7.41150.25051530.21267326747999
7.4115-8.15440.22861480.274057553100
8.1544-9.32770.22881500.192573777527100
9.3277-11.72640.22541530.19387351750499
11.7264-49.75450.25551450.2717168731397

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