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- PDB-5xj0: T. thermophilus RNA polymerase holoenzyme bound with gp39 and gp76 -

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Basic information

Entry
Database: PDB / ID: 5xj0
TitleT. thermophilus RNA polymerase holoenzyme bound with gp39 and gp76
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA polymerase sigma factor SigA
  • gp39
  • gp76
KeywordsTRANSFERASE/TRANSCRIPTION / Transcription regulation by bacteriophage-encoded proteins / TRANSFERASE-TRANSCRIPTION 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 / metal ion binding / cytoplasm
Similarity search - Function
SH3 type barrels. - #1250 / : / Thermus phage P23-45 gp39, N-terminal domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / 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 ...SH3 type barrels. - #1250 / : / Thermus phage P23-45 gp39, N-terminal domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / 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, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / 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 / : / 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 / Beta Complex / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / SH3 type barrels. / 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, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / 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 Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Thermus phage P23-45 gp39 N-terminal domain-containing protein / Uncharacterized protein / DNA-directed RNA polymerase subunit alpha / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesThermus virus P23-45
Thermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.004 Å
AuthorsOoi, W.Y. / Murayama, Y. / Mekler, V. / Minakhin, L. / Severinov, K. / Yokoyama, S. / Sekine, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPSJP23370048 Japan
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation
Authors: Ooi, W.Y. / Murayama, Y. / Mekler, V. / Minakhin, L. / Severinov, K. / Yokoyama, S. / Sekine, S.I.
History
DepositionApr 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 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: 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 SigA
G: gp39
H: gp39
Y: gp76
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,88910
Polymers465,8249
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47110 Å2
ΔGint-206 kcal/mol
Surface area161080 Å2
Unit cell
Length a, b, c (Å)294.427, 294.427, 222.774
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE

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


Mass: 35056.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: Q5SHR6, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 125436.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: Q8RQE9, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 170997.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: Q8RQE8, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 11533.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: Q8RQE7, DNA-directed RNA polymerase

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Protein , 3 types, 4 molecules FGHY

#5: Protein RNA polymerase sigma factor SigA


Mass: 48598.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: Q5SKW1
#6: Protein gp39


Mass: 16515.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus virus P23-45 / Production host: Escherichia coli (E. coli) / References: UniProt: A7XX65
#7: Protein gp76


Mass: 6114.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus virus P23-45 / Production host: Escherichia coli (E. coli) / References: UniProt: A7XXA7

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Non-polymers , 1 types, 1 molecules

#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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: 5.98 Å3/Da / Density % sol: 79.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50% tacsimate

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 93258 / % possible obs: 99.6 % / Redundancy: 9.6 % / Biso Wilson estimate: 121.81 Å2 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.085 / Rrim(I) all: 0.213 / Χ2: 0.874 / Net I/σ(I): 2.9 / Num. measured all: 890829
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)CC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
4-4.148.40.6530.6550.863100
4.14-4.318.30.7590.490.878100
4.31-4.58.20.8320.3360.89299.20.9220.984
4.5-4.749.30.9050.2670.998.90.7810.826
4.74-5.0410.30.9430.2290.8931000.7070.743
5.04-5.4310.40.9470.1980.9011000.6140.646
5.43-5.979.80.9570.1540.89999.30.4610.487
5.97-6.8410.50.980.1010.89799.50.3130.329
6.84-8.610.20.9970.040.8891000.1230.13
8.6-50100.9990.0170.73298.80.0510.054

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
SCALEPACKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WOD

3wod


Resolution: 4.004→49.777 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2715 4643 5.01 %
Rwork0.2368 87981 -
obs0.2386 92624 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 405.52 Å2 / Biso mean: 160.5078 Å2 / Biso min: 31.12 Å2
Refinement stepCycle: final / Resolution: 4.004→49.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29176 0 1 0 29177
Biso mean--225.96 --
Num. residues----3693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00829715
X-RAY DIFFRACTIONf_angle_d1.34340214
X-RAY DIFFRACTIONf_chiral_restr0.0624528
X-RAY DIFFRACTIONf_plane_restr0.0095277
X-RAY DIFFRACTIONf_dihedral_angle_d11.8811435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.0037-4.04920.33511390.3212843298296
4.0492-4.09680.35271540.32682914306899
4.0968-4.14680.36541550.31812939309499
4.1468-4.19920.34221590.31192881304099
4.1992-4.25440.33081520.29872910306299
4.2544-4.31270.31031660.29742929309599
4.3127-4.37430.2831450.28242904304999
4.3743-4.43950.2941440.27942902304699
4.4395-4.50890.31430.27072822296596
4.5089-4.58270.30541280.2722773290194
4.5827-4.66170.28021520.262929693121100
4.6617-4.74640.30791760.248329023078100
4.7464-4.83760.33831610.24232957311899
4.8376-4.93630.29471560.246729223078100
4.9363-5.04350.28651500.247129463096100
5.0435-5.16070.27611600.24242944310499
5.1607-5.28960.30061690.24729183087100
5.2896-5.43250.28241480.24129613109100
5.4325-5.59210.31811470.234829423089100
5.5921-5.77240.2771780.229629293107100
5.7724-5.97840.28251370.22992890302798
5.9784-6.21730.26181500.22732914306498
6.2173-6.49970.2851570.227329753132100
6.4997-6.84150.26191490.215729943143100
6.8415-7.2690.24921690.203229273096100
7.269-7.82820.25141610.204730063167100
7.8282-8.61230.20361470.182130173164100
8.6123-9.85020.17311450.17522939308498
9.8502-12.37860.19071790.173630253204100
12.3786-49.78040.31361670.27063087325499

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