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- PDB-1l9z: Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promote... -

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Basic information

Entry
Database: PDB / ID: 1l9z
TitleThermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution
Components
  • (RNA POLYMERASE, ...) x 4
  • SIGMA FACTOR SIGA
  • nontemplate DNA strand
  • template DNA strand
KeywordsTRANSCRIPTION/DNA / helix-turn-helix / coiled-coil / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
: / DNA-directed RNA polymerase subunit beta', hybrid domain / 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. ...: / DNA-directed RNA polymerase subunit beta', hybrid domain / 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
DNA / DNA (> 10) / DNA-directed RNA polymerase subunit omega / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 6.5 Å
AuthorsMurakami, K.S. / Masuda, S. / Campbell, E.A. / Muzzin, O. / Darst, S.A.
CitationJournal: Science / Year: 2002
Title: Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex.
Authors: Murakami, K.S. / Masuda, S. / Campbell, E.A. / Muzzin, O. / Darst, S.A.
History
DepositionMar 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
U: nontemplate DNA strand
T: template DNA strand
A: RNA POLYMERASE, ALPHA SUBUNIT
B: RNA POLYMERASE, ALPHA SUBUNIT
C: RNA POLYMERASE, BETA SUBUNIT
D: RNA POLYMERASE, BETA-PRIME SUBUNIT
E: RNA POLYMERASE, OMEGA SUBUNIT
H: SIGMA FACTOR SIGA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)447,34011
Polymers447,1848
Non-polymers1553
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.947, 180.947, 523.461
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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DNA chain , 2 types, 2 molecules UT

#1: DNA chain nontemplate DNA strand


Mass: 10801.969 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain template DNA strand


Mass: 9166.931 Da / Num. of mol.: 1 / Source method: obtained synthetically

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RNA POLYMERASE, ... , 4 types, 5 molecules ABCDE

#3: Protein RNA POLYMERASE, ALPHA SUBUNIT


Mass: 34830.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU8, DNA-directed RNA polymerase
#4: Protein RNA POLYMERASE, BETA SUBUNIT


Mass: 124800.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU7, DNA-directed RNA polymerase
#5: Protein RNA POLYMERASE, BETA-PRIME SUBUNIT


Mass: 171187.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU6, DNA-directed RNA polymerase
#6: Protein RNA POLYMERASE, OMEGA SUBUNIT


Mass: 11642.423 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9EVV4, DNA-directed RNA polymerase

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Protein , 1 types, 1 molecules H

#7: Protein SIGMA FACTOR SIGA


Mass: 49922.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: rpoD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9EZJ8

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Non-polymers , 2 types, 3 molecules

#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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: 4.78 Å3/Da / Density % sol: 74.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, Tris, Magnesium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2Tris11
3MgCl211
Crystal
*PLUS
Density % sol: 75 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
21.6-1.8 Mammonium sulfate1reservoir
30.1 MTris-HCl1reservoirpH8.0
420 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.94799 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94799 Å / Relative weight: 1
ReflectionResolution: 6.5→80 Å / Num. all: 17816 / Num. obs: 16195 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.5
Reflection shellResolution: 6.5→6.73 Å / Redundancy: 2.4 % / Rsym value: 0.241 / % possible all: 78.5
Reflection
*PLUS
Lowest resolution: 80 Å / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 78.5 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameClassification
MLPHAREphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 6.5→80 Å / Num. reflection obs: 16195
Refinement stepCycle: LAST / Resolution: 6.5→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9366 709 3 0 10078
Refinement
*PLUS
Lowest resolution: 80 Å / Rfactor obs: 0.448 / Rfactor Rfree: 0.452 / Rfactor Rwork: 0.448
Solvent computation
*PLUS
Displacement parameters
*PLUS

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