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- PDB-1xs9: A MODEL OF THE TERNARY COMPLEX FORMED BETWEEN MARA, THE ALPHA-CTD... -

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Entry
Database: PDB / ID: 1xs9
TitleA MODEL OF THE TERNARY COMPLEX FORMED BETWEEN MARA, THE ALPHA-CTD OF RNA POLYMERASE AND DNA
Components
  • 5'-D(P*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP*AP*AP*TP*C)-3'
  • 5'-D(P*GP*AP*TP*TP*TP*AP*GP*CP*AP*AP*AP*AP*CP*GP*TP*GP*GP*CP*AP*T)-3'
  • DNA-directed RNA polymerase alpha chain
  • Multiple antibiotic resistance protein marA
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TERNARY COMPLEX / MARA / RNA POLYMERASE / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


bacterial-type RNA polymerase holo enzyme binding / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation / regulation of DNA-templated transcription elongation / transcription elongation factor complex ...bacterial-type RNA polymerase holo enzyme binding / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / 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 / DNA-templated transcription initiation / cell motility / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to heat / sequence-specific DNA binding / intracellular iron ion homeostasis / protein dimerization activity / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeodomain-like / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain ...: / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeodomain-like / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / 5' to 3' exonuclease, C-terminal subdomain / Homeobox-like domain 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / DNA polymerase; domain 1 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-directed RNA polymerase subunit alpha / Multiple antibiotic resistance protein MarA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / MODEL BASED ON CHEMICAL SHIFT PERTURBATION MAPPING
AuthorsDangi, B. / Gronenborn, A.M. / Rosner, J.L. / Martin, R.G.
CitationJournal: Mol.Microbiol. / Year: 2004
Title: Versatility of the carboxy-terminal domain of the alpha subunit of RNA polymerase in transcriptional activation: use of the DNA contact site as a protein contact site for MarA.
Authors: Dangi, B. / Gronenborn, A.M. / Rosner, J.L. / Martin, R.G.
History
DepositionOct 18, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionOct 26, 2004ID: 1TI9
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-D(P*GP*AP*TP*TP*TP*AP*GP*CP*AP*AP*AP*AP*CP*GP*TP*GP*GP*CP*AP*T)-3'
C: 5'-D(P*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP*AP*AP*TP*C)-3'
A: Multiple antibiotic resistance protein marA
D: DNA-directed RNA polymerase alpha chain


Theoretical massNumber of molelcules
Total (without water)37,2814
Polymers37,2814
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 200
RepresentativeModel #1

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Components

#1: DNA chain 5'-D(P*GP*AP*TP*TP*TP*AP*GP*CP*AP*AP*AP*AP*CP*GP*TP*GP*GP*CP*AP*T)-3'


Mass: 6182.029 Da / Num. of mol.: 1 / Fragment: PROMOTER REGION / Source method: obtained synthetically
#2: DNA chain 5'-D(P*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP*AP*AP*TP*C)-3'


Mass: 6083.953 Da / Num. of mol.: 1 / Fragment: PROMOTER REGION / Source method: obtained synthetically
#3: Protein Multiple antibiotic resistance protein marA


Mass: 15723.780 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: marA / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: P0ACH5
#4: Protein DNA-directed RNA polymerase alpha chain / RNAP alpha subunit / Transcriptase alpha chain / RNA polymerase alpha subunit


Mass: 9291.663 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, pez, phs, sez / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P0A7Z4, DNA-directed RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: HSQC

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Sample preparation

DetailsContents: AS DESCRIBED IN PAPER
Sample conditionspH: 6.7 / Temperature units: K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameDeveloperClassification
HADDOCKJONES,ZOU,COWAN,KJELDGAARDrefinement
NMRPipestructure solution
XwinNMRstructure solution
HADDOCKstructure solution
RefinementMethod: MODEL BASED ON CHEMICAL SHIFT PERTURBATION MAPPING / Software ordinal: 1 / Details: Program HADDOCK was used to generate the nodels
NMR ensembleConformers calculated total number: 200 / Conformers submitted total number: 1

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