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- PDB-4zh4: Crystal structure of Escherichia coli RNA polymerase in complex w... -

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Basic information

Entry
Database: PDB / ID: 4zh4
TitleCrystal structure of Escherichia coli RNA polymerase in complex with CBRP18
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
Helix Hairpins - #1670 / DNA polymerase; domain 1 - #390 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region ...Helix Hairpins - #1670 / DNA polymerase; domain 1 - #390 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / 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 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Sigma-70 factors family signature 1. / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Helix Hairpins / : / 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 / 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 / 5' to 3' exonuclease, C-terminal subdomain / Helix non-globular / Beta Complex / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / 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
Similarity search - Domain/homology
Chem-4OE / 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: 3.993 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)924,08820
Polymers923,12912
Non-polymers9598
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)462,04410
Polymers461,5656
Non-polymers4794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38920 Å2
ΔGint-179 kcal/mol
Surface area160510 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)462,04410
Polymers461,5656
Non-polymers4794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38250 Å2
ΔGint-180 kcal/mol
Surface area162300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.581, 204.105, 308.038
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-4OE / 5-(4-fluorophenyl)-4-[4-fluoro-3-(trifluoromethyl)phenyl]-1H-pyrazole


Mass: 324.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H9F5N2
#7: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 61.21 %
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 30, 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→50 Å / Num. obs: 99049 / % possible obs: 100 % / Redundancy: 14.4 % / Biso Wilson estimate: 156.41 Å2 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.048 / Rrim(I) all: 0.179 / Χ2: 1.111 / Net I/av σ(I): 14.636 / Net I/σ(I): 6.2 / Num. measured all: 1430622
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
4-4.0713.80.99848870.8580.2770.946100
4.07-4.1414.70.78548950.910.2110.9811000.813
4.14-4.2214.70.69849020.9270.1871.0071000.723
4.22-4.3114.70.58948910.9380.1581.0471000.61
4.31-4.414.70.52549020.950.1411.081000.543
4.4-4.514.70.46148820.960.1241.1141000.478
4.5-4.6214.70.40249220.9680.1081.151000.417
4.62-4.7414.70.36849200.9680.0991.1891000.381
4.74-4.8814.70.3449140.9720.0911.1951000.352
4.88-5.0414.70.32749280.9730.0871.1881000.338
5.04-5.2214.70.30349330.9780.0811.1661000.314
5.22-5.4314.60.28549120.9780.0771.1761000.296
5.43-5.6714.60.26549390.980.0711.1661000.274
5.67-5.9714.60.24549620.9830.0661.1671000.254
5.97-6.3514.50.22449320.9850.061.1761000.232
6.35-6.8414.40.19849800.9860.0531.1881000.205
6.84-7.5214.30.17950080.9880.0481.2151000.185
7.52-8.614.20.16550080.9880.0451.2351000.171
8.6-10.8213.70.1450680.9930.0391.0251000.145
10.82-50130.10652640.9850.0310.77199.80.11

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4LK1

4lk1


Resolution: 3.993→49.2 Å / FOM work R set: 0.7504 / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2829 1858 2 %
Rwork0.2497 91013 -
obs0.2504 92871 93.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 401.51 Å2 / Biso mean: 116.04 Å2 / Biso min: 0.02 Å2
Refinement stepCycle: final / Resolution: 3.993→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms57487 0 52 0 57539
Biso mean--91.46 --
Num. residues----7357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00558362
X-RAY DIFFRACTIONf_angle_d0.98878802
X-RAY DIFFRACTIONf_chiral_restr0.0649006
X-RAY DIFFRACTIONf_plane_restr0.00510333
X-RAY DIFFRACTIONf_dihedral_angle_d16.62922411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.9931-4.1010.34741110.32795585569675
4.101-4.22160.36111330.30496471660487
4.2216-4.35780.35281340.29386599673389
4.3578-4.51350.30081370.28526727686490
4.5135-4.69410.32791370.26386822695992
4.6941-4.90750.31011460.25666983712994
4.9075-5.1660.2981450.26767084722995
5.166-5.48930.33161470.26147192733996
5.4893-5.91240.32651480.2677285743397
5.9124-6.50620.31451520.26247397754998
6.5062-7.44490.26671550.24547507766299
7.4449-9.36920.23481560.2176167772100
9.3692-49.20410.24961570.23347745790298

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