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- PDB-7egs: The crystal structure of lobe domain of E. coli RNA polymerase co... -

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Basic information

Entry
Database: PDB / ID: 7egs
TitleThe crystal structure of lobe domain of E. coli RNA polymerase complexed with the C-terminal domain of UvrD
Components
  • DNA helicase IIHelicase
  • DNA-directed RNA polymerase subunit betaPolymerase
KeywordsTRANSCRIPTION / TCR / Escherichia Coli / UvrD / RNA polymerase / DNA repair
Function / homology
Function and homology information


rolling circle DNA replication / single-stranded DNA-dependent ATP-dependent DNA helicase complex / DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / nucleotide-excision repair, DNA duplex unwinding / DNA 3'-5' helicase / DNA translocase activity / single-stranded DNA helicase activity / recombinational repair / SOS response ...rolling circle DNA replication / single-stranded DNA-dependent ATP-dependent DNA helicase complex / DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / nucleotide-excision repair, DNA duplex unwinding / DNA 3'-5' helicase / DNA translocase activity / single-stranded DNA helicase activity / recombinational repair / SOS response / 3'-5' DNA helicase activity / DNA duplex unwinding / replication fork processing / submerged biofilm formation / DNA unwinding involved in DNA replication / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / mismatch repair / nitrate assimilation / isomerase activity / DNA helicase activity / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / nucleotide-excision repair / DNA-templated transcription initiation / response to radiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / intracellular iron ion homeostasis / response to antibiotic / ATP hydrolysis activity / protein homodimerization activity / DNA binding / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
DNA helicase, ATP-dependent, UvrD type / PcrA/UvrD tudor domain / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type ...DNA helicase, ATP-dependent, UvrD type / PcrA/UvrD tudor domain / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP 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 / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase beta 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA helicase II / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZheng, F. / Shen, L. / Li, L. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31670067 China
CitationJournal: Nature / Year: 2022
Title: Crucial role and mechanism of transcription-coupled DNA repair in bacteria.
Authors: Bharati, B.K. / Gowder, M. / Zheng, F. / Alzoubi, K. / Svetlov, V. / Kamarthapu, V. / Weaver, J.W. / Epshtein, V. / Vasilyev, N. / Shen, L. / Zhang, Y. / Nudler, E.
History
DepositionMar 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Apr 20, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 beta
B: DNA helicase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7543
Polymers41,6612
Non-polymers921
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.085, 42.241, 87.849
Angle α, β, γ (deg.)90.000, 105.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33931.730 Da / Num. of mol.: 1
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 BL21(DE3) (bacteria) / References: UniProt: P0A8V2, DNA-directed RNA polymerase
#2: Protein DNA helicase II / Helicase


Mass: 7729.751 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: uvrD, mutU, pdeB, rad, recL, b3813, JW3786 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03018, DNA helicase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.0, 10% w/v polyethylene glycol 4000, 10 % (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 46583 / % possible obs: 98.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 29.57 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.041 / Rrim(I) all: 0.077 / Χ2: 1.137 / Net I/av σ(I): 16.3 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.733.20.40522940.8530.2630.4850.63499.4
1.73-1.763.30.35223560.8740.2290.4220.62599.2
1.76-1.793.30.323090.9230.1940.3590.67499.5
1.79-1.833.30.25523180.9450.1650.3050.70399.3
1.83-1.873.30.21523060.9490.1390.2570.75499
1.87-1.913.30.18623260.9610.1210.2220.81698.6
1.91-1.963.10.15722320.9540.1050.190.9797.2
1.96-2.023.50.12923240.9790.0810.1530.98599.4
2.02-2.073.40.11923340.9790.0750.1411.10599.3
2.07-2.143.40.10923410.9830.0690.131.2499.4
2.14-2.223.40.10123660.9840.0650.1211.31199.4
2.22-2.313.20.09522860.9810.0620.1141.45899
2.31-2.413.20.08923010.9890.0560.1051.53997.7
2.41-2.543.50.08523240.9870.0530.11.45499.5
2.54-2.73.40.07823530.9860.050.0931.50499.4
2.7-2.913.40.07623530.9870.0480.091.61199.2
2.91-3.23.30.07323150.9860.0470.0871.62197.9
3.2-3.663.50.06723530.9910.0420.0791.61599.2
3.66-4.613.20.05623590.9920.0360.0671.26897.8
4.61-403.40.04724330.9910.030.0560.76898.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LTI

3lti


Resolution: 1.7→37.807 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 2439 5.34 %
Rwork0.2032 43254 -
obs0.2048 45693 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.83 Å2 / Biso mean: 38.6115 Å2 / Biso min: 19.14 Å2
Refinement stepCycle: final / Resolution: 1.7→37.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2705 0 6 161 2872
Biso mean--49.61 40.14 -
Num. residues----348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082776
X-RAY DIFFRACTIONf_angle_d1.0583749
X-RAY DIFFRACTIONf_chiral_restr0.044420
X-RAY DIFFRACTIONf_plane_restr0.006489
X-RAY DIFFRACTIONf_dihedral_angle_d12.4171038
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.73470.33721480.2841254798
1.7347-1.77240.30451350.2657260599
1.7724-1.81370.29661350.244257499
1.8137-1.8590.30731530.2409252398
1.859-1.90930.28091400.2371256697
1.9093-1.96540.29171230.2275248795
1.9654-2.02890.20991490.2237259298
2.0289-2.10140.25261510.2319255398
2.1014-2.18550.25521490.2175253598
2.1855-2.2850.26451490.2216254697
2.285-2.40540.2531530.2103249495
2.4054-2.55610.28531540.2288253897
2.5561-2.75340.24971540.2219255297
2.7534-3.03040.23331540.2234252396
3.0304-3.46860.22661450.1996253396
3.4686-4.36910.20081300.176254595
4.3691-37.8070.18851170.1721254192

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