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- PDB-5ciz: E. coli RNA polymerase alpha subunit CTD in complex with CAP and ... -

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Basic information

Entry
Database: PDB / ID: 5ciz
TitleE. coli RNA polymerase alpha subunit CTD in complex with CAP and DNA: A(5)-tract binding site for alpha CTD
Components
  • DNA (5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*CP*AP*AP*AP*AP*AP*G)-3')
  • DNA (5'-D(*CP*TP*TP*TP*TP*TP*GP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3')
  • DNA-directed RNA polymerase subunit alphaPolymerase
  • cAMP-activated global transcriptional regulator CRP
KeywordsGene regulation/DNA / protein-protein interactions / protein-DNA interactions / gene regulation-DNA complex / knock out
Function / homology
Function and homology information


carbon catabolite repression of transcription / DNA binding, bending / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / minor groove of adenine-thymine-rich DNA binding / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...carbon catabolite repression of transcription / DNA binding, bending / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / minor groove of adenine-thymine-rich DNA binding / bacterial-type flagellum-dependent cell motility / nitrate assimilation / cAMP binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / protein-DNA complex / DNA-templated transcription initiation / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / intracellular iron ion homeostasis / sequence-specific DNA binding / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain ...Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / RmlC-like jelly roll fold / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / DNA / DNA (> 10) / DNA-directed RNA polymerase subunit alpha / DNA-binding transcriptional dual regulator CRP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.0098 Å
AuthorsNapoli, A.A. / Lawson, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM21589 United States
CitationJournal: Biochemistry / Year: 2020
Title: The RNA Polymerase alpha Subunit Recognizes the DNA Shape of the Upstream Promoter Element
Authors: Lara-Gonzalez, S. / Machado, A.C.D. / Rao, S. / Napoli, A.A. / Birktoft, J. / Di Felice, R. / Rohs, R. / Lawson, C.L.
History
DepositionJul 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
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 / 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: cAMP-activated global transcriptional regulator CRP
B: DNA-directed RNA polymerase subunit alpha
D: DNA (5'-D(*CP*TP*TP*TP*TP*TP*GP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3')
E: DNA (5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*CP*AP*AP*AP*AP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7355
Polymers46,4064
Non-polymers3291
Water0
1
A: cAMP-activated global transcriptional regulator CRP
B: DNA-directed RNA polymerase subunit alpha
D: DNA (5'-D(*CP*TP*TP*TP*TP*TP*GP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3')
E: DNA (5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*CP*AP*AP*AP*AP*AP*G)-3')
hetero molecules

A: cAMP-activated global transcriptional regulator CRP
B: DNA-directed RNA polymerase subunit alpha
D: DNA (5'-D(*CP*TP*TP*TP*TP*TP*GP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3')
E: DNA (5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*CP*AP*AP*AP*AP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,47010
Polymers92,8128
Non-polymers6582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_657-x+y+1,y,-z+21
Buried area13570 Å2
ΔGint-94 kcal/mol
Surface area40150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.312, 176.312, 158.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein cAMP-activated global transcriptional regulator CRP / Catabolite activator protein / CAP / Catabolite gene activator / cAMP receptor protein / CRP / cAMP ...Catabolite activator protein / CAP / Catabolite gene activator / cAMP receptor protein / CRP / cAMP regulatory protein


Mass: 23541.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: crp, cap, csm, b3357, JW5702 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ACJ8
#2: Protein DNA-directed RNA polymerase subunit alpha / Polymerase / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 9364.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase
#3: DNA chain DNA (5'-D(*CP*TP*TP*TP*TP*TP*GP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3')


Mass: 6113.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain DNA (5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*CP*AP*AP*AP*AP*AP*G)-3')


Mass: 7385.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#5: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 28% (w/v) PEG4000, 0.2 M ammonium acetate, 0.01 M sarcosine, 0.1 M sodium citrate, pH 5.6
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 5.0098→50 Å / Num. obs: 6646 / % possible obs: 99.7 % / Redundancy: 18.7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.1
Reflection shellResolution: 5.0098→5.18 Å / Redundancy: 19.2 % / Rmerge(I) obs: 0.733 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LB2

1lb2


Resolution: 5.0098→49.927 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 663 10.02 %random
Rwork0.178 ---
obs0.1816 6615 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 5.0098→49.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 896 22 0 3099
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint function
X-RAY DIFFRACTIONf_bond_d0.0133243
X-RAY DIFFRACTIONf_angle_d1.664573
X-RAY DIFFRACTIONf_dihedral_angle_d23.0921286
X-RAY DIFFRACTIONf_chiral_restr0.074526
X-RAY DIFFRACTIONf_plane_restr0.008425
X-RAY DIFFRACTIONphenix.refine reference_model3N4M used as reference model
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.0098-5.39620.31521270.23121145X-RAY DIFFRACTION99
5.3962-5.93850.24471300.21031176X-RAY DIFFRACTION100
5.9385-6.79590.24391310.17821173X-RAY DIFFRACTION100
6.7959-8.55520.18551320.17951190X-RAY DIFFRACTION100
8.5552-49.92940.19621430.1621268X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 108.1332 Å / Origin y: -53.8316 Å / Origin z: 148.3464 Å
111213212223313233
T2.3502 Å20.092 Å2-0.0495 Å2-2.0826 Å2-0.0298 Å2--2.0273 Å2
L4.29 °20.2151 °2-0.791 °2-1.9922 °2-0.1293 °2--2.7134 °2
S0.0012 Å °0.0454 Å °0.5036 Å °0.1287 Å °-0.0102 Å °-0.3672 Å °-0.0082 Å °0.4145 Å °0.0143 Å °
Refinement TLS groupSelection details: (all)

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