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- PDB-2a69: Crystal structure of the T. Thermophilus RNA polymerase holoenzym... -

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Basic information

Entry
Database: PDB / ID: 2a69
TitleCrystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin
Components
  • (DNA-directed RNA polymerase ...Polymerase) x 3
  • (RNA polymerase ...) x 2
KeywordsTRANSFERASE / RNA POLYMERASE HOLOENZYME / RIFAPENTIN / ANTIBIOTIC / TRANSCRIPTION REGULATION / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 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 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Wheat Germ Agglutinin (Isolectin 2); domain 1 - #280 / Rna Polymerase Beta Subunit; Chain: C,domain 2 / Rna Polymerase Beta Subunit; Chain: C,domain 2 - #10 / 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 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain ...Wheat Germ Agglutinin (Isolectin 2); domain 1 - #280 / Rna Polymerase Beta Subunit; Chain: C,domain 2 / Rna Polymerase Beta Subunit; Chain: C,domain 2 - #10 / 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 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / Enzyme I; Chain A, domain 2 / Topoisomerase I; Chain A, domain 4 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Wheat Germ Agglutinin (Isolectin 2); domain 1 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / 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 / 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, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Four Helix Bundle (Hemerythrin (Met), subunit A) / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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
Similarity search - Domain/homology
RIFAPENTINE / : / : / 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 / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsArtsimovitch, I. / Vassylyeva, M.N. / Svetlov, D. / Svetlov, V. / Perederina, A. / Igarashi, N. / Matsugaki, N. / Wakatsuki, S. / Tahirov, T.H. / Vassylyev, D.G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins.
Authors: Artsimovitch, I. / Vassylyeva, M.N. / Svetlov, D. / Svetlov, V. / Perederina, A. / Igarashi, N. / Matsugaki, N. / Wakatsuki, S. / Tahirov, T.H. / Vassylyev, D.G.
History
DepositionJul 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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
A: DNA-directed RNA polymerase alpha chain
B: DNA-directed RNA polymerase alpha chain
C: DNA-directed RNA polymerase beta chain
D: DNA-directed RNA polymerase beta' chain
E: RNA polymerase omega chain
F: RNA polymerase sigma factor rpoD
K: DNA-directed RNA polymerase alpha chain
L: DNA-directed RNA polymerase alpha chain
M: DNA-directed RNA polymerase beta chain
N: DNA-directed RNA polymerase beta' chain
O: RNA polymerase omega chain
P: RNA polymerase sigma factor rpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)867,123505
Polymers853,27112
Non-polymers13,852493
Water115,2786399
1
A: DNA-directed RNA polymerase alpha chain
B: DNA-directed RNA polymerase alpha chain
C: DNA-directed RNA polymerase beta chain
D: DNA-directed RNA polymerase beta' chain
E: RNA polymerase omega chain
F: RNA polymerase sigma factor rpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)434,108275
Polymers426,6356
Non-polymers7,473269
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43410 Å2
ΔGint-160 kcal/mol
Surface area147150 Å2
MethodPISA
2
K: DNA-directed RNA polymerase alpha chain
L: DNA-directed RNA polymerase alpha chain
M: DNA-directed RNA polymerase beta chain
N: DNA-directed RNA polymerase beta' chain
O: RNA polymerase omega chain
P: RNA polymerase sigma factor rpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)433,015230
Polymers426,6356
Non-polymers6,379224
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43870 Å2
ΔGint-170 kcal/mol
Surface area146300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)239.500, 239.500, 253.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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DNA-directed RNA polymerase ... , 3 types, 8 molecules ABKLCMDN

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


Mass: 35056.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q9Z9H6, UniProt: Q5SHR6*PLUS, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase beta chain / RNAP beta subunit / Transcriptase beta chain / RNA polymerase beta subunit


Mass: 125436.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q8RQE9, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase beta' chain / RNAP beta' subunit / Transcriptase beta' chain / RNA polymerase beta' subunit


Mass: 170997.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q8RQE8, DNA-directed RNA polymerase

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RNA polymerase ... , 2 types, 4 molecules EOFP

#4: Protein RNA polymerase omega chain


Mass: 11521.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 20160394, UniProt: Q8RQE7*PLUS
#5: Protein RNA polymerase sigma factor rpoD


Mass: 48568.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 46198472, UniProt: Q5SKW1*PLUS

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Non-polymers , 4 types, 6892 molecules

#6: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 487 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-RPT / RIFAPENTINE / (2R,16S,17R,18R,19R,20S,21S,22S,23S)-8-{[(4-CYCLOPENTYLPIPERAZIN-1-YL)IMINO]METHYL}-5,6,9,17,19-PENTAHYDROXY-23-METHOXY -2,4,12,16,18,20,22-HEPTAMETHYL-1,11-DIOXO-1,2-DIHYDRO-2,7-(EPOXYPENTADECA[1,11,13]TRIENOIMINO)NAPHTHO[2,1-B]FURAN-21-YL ACETATE / 3-(((4-CYCLOPENTYL-1-PIPERAZINYL)IMINO)METHYL)RIFAMYCIN / Rifapentine


Mass: 877.031 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H64N4O12 / Comment: medication, antibiotic*YM
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6399 / Source method: isolated from a natural source / Formula: H2O

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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: 5.2 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MG FORMATE, PEG400, SPERMIDINE, TRIS HCL, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 560482 / Num. obs: 517106 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.37 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.35 / % possible all: 81.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IW7

1iw7


Resolution: 2.5→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (-H,-K,L) AND THE TWINNING FRACTION IS 0.5. THE R-FACTOR IS 0.230 AND THE R-FREE IS 0.267 WHEN THIS TWINNING OPERATOR IS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 29710 5.3 %RANDOM
Rwork0.23 ---
all0.235 517106 --
obs0.23 517106 --
Displacement parametersBiso mean: 72.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53556 0 617 6399 60572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.88
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.72
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.356 2498 4.4 %
Rwork0.339 40578 -
obs--72.4 %

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