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- PDB-4oir: Crystal structure of Thermus thermophilus RNA polymerase transcri... -

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Basic information

Entry
Database: PDB / ID: 4oir
TitleCrystal structure of Thermus thermophilus RNA polymerase transcription initiation complex soaked with GE23077 and rifamycin SV
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • 5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3'
  • 5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3'
  • DNA directed RNA polymerase sigma factor A
  • GE23077
KeywordsTRANSCRIPTION / TRANSFERASE/ANTIBIOTIC / GE23077 / transcription inhibitor / transcription open complex / transcription initiation complex / rifamycin SV / i site / i+1 site / RNA polymerase / DNA/RNA/NTP binding / polymerization of ribonucleotides / nucleoid / TRANSFERASE-ANTIBIOTIC 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
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1810 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1810 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / 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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Beta Complex / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Roll / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / 2-Layer Sandwich
Similarity search - Domain/homology
GE23077 / (2Z)-2-methylbut-2-enoic acid / rifamycin SV / DNA / DNA (> 10) / 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 thermophilus (bacteria)
Actinomadura sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.105 Å
AuthorsZhang, Y. / Ebright, R.H. / Arnold, E.
CitationJournal: Elife / Year: 2014
Title: GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.
Authors: Zhang, Y. / Degen, D. / Ho, M.X. / Sineva, E. / Ebright, K.Y. / Ebright, Y.W. / Mekler, V. / Vahedian-Movahed, H. / Feng, Y. / Yin, R. / Tuske, S. / Irschik, H. / Jansen, R. / Maffioli, S. / ...Authors: Zhang, Y. / Degen, D. / Ho, M.X. / Sineva, E. / Ebright, K.Y. / Ebright, Y.W. / Mekler, V. / Vahedian-Movahed, H. / Feng, Y. / Yin, R. / Tuske, S. / Irschik, H. / Jansen, R. / Maffioli, S. / Donadio, S. / Arnold, E. / Ebright, R.H.
History
DepositionJan 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Non-polymer description
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 13, 2025Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: DNA directed RNA polymerase sigma factor A
G: 5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3'
H: 5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3'
I: GE23077
hetero molecules


Theoretical massNumber of molelcules
Total (without water)443,16317
Polymers442,1359
Non-polymers1,0288
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.700, 105.010, 295.360
Angle α, β, γ (deg.)90.00, 98.79, 90.00
Int Tables number5
Space group name H-MC121

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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: 33878.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / 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 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / 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 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / 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 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8RQE7, DNA-directed RNA polymerase

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DNA chain , 2 types, 2 molecules GH

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


Mass: 6480.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: promoter DNA template strand
#7: DNA chain 5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3'


Mass: 8421.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: promoter DNA nontemplate strand

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Protein / Protein/peptide , 2 types, 2 molecules FI

#5: Protein DNA directed RNA polymerase sigma factor A / RNA polymerase sigma factor


Mass: 50769.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: rpoD, TTHA0532 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKW1
#8: Protein/peptide GE23077


Type: Cyclic peptide / Class: Antibiotic, Antimicrobial / Mass: 739.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Actinomadura sp. (bacteria) / References: GE23077

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Non-polymers , 5 types, 131 molecules

#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-RFV / rifamycin SV


Mass: 699.784 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H49NO12
#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#12: Chemical ChemComp-MB8 / (2Z)-2-methylbut-2-enoic acid


Type: Cyclic peptide / Class: Antibiotic, Antimicrobial / Mass: 100.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O2 / References: GE23077
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 100 mM Tris-HCl, pH 8.4, 200 mM potassium chloride, 50 mM magnesium chloride, 9.5% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 101511 / Num. obs: 98567 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 63.48 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 7.6
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 1.3 / Num. unique all: 3894 / Rsym value: 0.727 / % possible all: 77.9

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G7H

4g7h


Resolution: 3.105→47.496 Å / SU ML: 0.41 / Isotropic thermal model: ISOTROPIC / σ(F): 1.33 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 4159 5 %RANDOM
Rwork0.2063 ---
obs0.2087 83131 82.64 %-
all-100594 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.4 Å2
Refinement stepCycle: LAST / Resolution: 3.105→47.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27718 823 58 123 28722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00429216
X-RAY DIFFRACTIONf_angle_d0.81339677
X-RAY DIFFRACTIONf_dihedral_angle_d14.28811314
X-RAY DIFFRACTIONf_chiral_restr0.0664468
X-RAY DIFFRACTIONf_plane_restr0.0045056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.105-3.14050.3160.3245215X-RAY DIFFRACTION7
3.1405-3.17740.3056260.2963519X-RAY DIFFRACTION16
3.1774-3.21620.3769330.3267808X-RAY DIFFRACTION25
3.2162-3.25690.3013590.30841176X-RAY DIFFRACTION37
3.2569-3.29970.3201810.29941540X-RAY DIFFRACTION48
3.2997-3.34490.3551930.31725X-RAY DIFFRACTION56
3.3449-3.39270.32491230.30782016X-RAY DIFFRACTION63
3.3927-3.44330.31511140.29982275X-RAY DIFFRACTION71
3.4433-3.49710.3371340.2932448X-RAY DIFFRACTION78
3.4971-3.55440.3411460.2792706X-RAY DIFFRACTION86
3.5544-3.61570.33911450.26822897X-RAY DIFFRACTION91
3.6157-3.68140.32521740.25693101X-RAY DIFFRACTION99
3.6814-3.75220.34811600.24513209X-RAY DIFFRACTION100
3.7522-3.82880.29381710.23433140X-RAY DIFFRACTION100
3.8288-3.9120.30361640.2263199X-RAY DIFFRACTION100
3.912-4.00290.27361730.21623144X-RAY DIFFRACTION100
4.0029-4.1030.26241630.20383184X-RAY DIFFRACTION100
4.103-4.21380.2761680.19773211X-RAY DIFFRACTION100
4.2138-4.33780.22761660.19133139X-RAY DIFFRACTION100
4.3378-4.47770.23451680.17643196X-RAY DIFFRACTION100
4.4777-4.63760.22981590.17753194X-RAY DIFFRACTION100
4.6376-4.82310.21931730.17393198X-RAY DIFFRACTION100
4.8231-5.04240.211720.17733176X-RAY DIFFRACTION100
5.0424-5.30790.26111660.18293195X-RAY DIFFRACTION100
5.3079-5.63990.24581660.1873163X-RAY DIFFRACTION100
5.6399-6.07460.24371620.19663218X-RAY DIFFRACTION100
6.0746-6.68440.24961650.19323218X-RAY DIFFRACTION100
6.6844-7.64820.24061730.18093217X-RAY DIFFRACTION100
7.6482-9.62270.1771690.15613268X-RAY DIFFRACTION100
9.6227-47.50130.17561770.17933277X-RAY DIFFRACTION99

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