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- PDB-2cw0: Crystal structure of Thermus thermophilus RNA polymerase holoenzy... -

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Basic information

Entry
Database: PDB / ID: 2cw0
TitleCrystal structure of Thermus thermophilus RNA polymerase holoenzyme at 3.3 angstroms resolution
Components
  • (DNA-directed RNA polymerase ...Polymerase) x 3
  • (RNA polymerase ...) x 2
KeywordsTRANSFERASE / RNA polymerase holoenzyme / transcription / bent-bridge helix
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
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 ...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 / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / 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 / 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 / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex
Similarity search - Domain/homology
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsTuske, S. / Sarafianos, S.G. / Wang, X. / Hudson, B. / Sineva, E. / Mukhopadhyay, J. / Birktoft, J.J. / Leroy, O. / Ismail, S. / Clark Jr., A.D. ...Tuske, S. / Sarafianos, S.G. / Wang, X. / Hudson, B. / Sineva, E. / Mukhopadhyay, J. / Birktoft, J.J. / Leroy, O. / Ismail, S. / Clark Jr., A.D. / Dharia, C. / Napoli, A. / Laptenko, O. / Lee, J. / Borukhov, S. / Ebright, R.H. / Arnold, E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation
Authors: Tuske, S. / Sarafianos, S.G. / Wang, X. / Hudson, B. / Sineva, E. / Mukhopadhyay, J. / Birktoft, J.J. / Leroy, O. / Ismail, S. / Clark Jr., A.D. / Dharia, C. / Napoli, A. / Laptenko, O. / ...Authors: Tuske, S. / Sarafianos, S.G. / Wang, X. / Hudson, B. / Sineva, E. / Mukhopadhyay, J. / Birktoft, J.J. / Leroy, O. / Ismail, S. / Clark Jr., A.D. / Dharia, C. / Napoli, A. / Laptenko, O. / Lee, J. / Borukhov, S. / Ebright, R.H. / Arnold, E.
History
DepositionJun 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Sep 5, 2012Group: Refinement description
Revision 1.4Dec 4, 2019Group: Derived calculations / Category: struct_conn / struct_conn_type
Revision 1.5Oct 25, 2023Group: Data collection / Database references ...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 / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.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_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)853,58118
Polymers853,27112
Non-polymers3106
Water0
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)426,7919
Polymers426,6356
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43720 Å2
ΔGint-219 kcal/mol
Surface area148220 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)426,7919
Polymers426,6356
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)236.150, 236.150, 249.880
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 / DNA directed RNA polymerase holoenzyme subunit alpha / RNAP alpha subunit / Transcriptase alpha ...DNA directed RNA polymerase holoenzyme subunit alpha / 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: Q5SHR6, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase beta chain / DNA directed RNA polymerase holoenzyme subunit Beta / RNAP beta subunit / Transcriptase beta chain ...DNA directed RNA polymerase holoenzyme subunit Beta / 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) / Strain: HB8 / References: UniProt: Q8RQE9, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase beta' chain / DNA directed RNA polymerase holoenzyme subunit Beta-prime / RNAP beta' subunit / Transcriptase ...DNA directed RNA polymerase holoenzyme subunit Beta-prime / 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) / Strain: HB8 / References: UniProt: Q8RQE8, DNA-directed RNA polymerase

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

#4: Protein RNA polymerase omega chain / DNA directed RNA polymerase holoenzyme subunit Omega


Mass: 11521.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q8RQE7, DNA-directed RNA polymerase
#5: Protein RNA polymerase sigma factor rpoD / DNA directed RNA polymerase holoenzyme subunit Sigma


Mass: 48568.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q5SKW1, DNA-directed RNA polymerase

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Non-polymers , 2 types, 6 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 4.54 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.85
Details: 33mM magnesium formate over a reservoir of 33mM magnesium formate, 30mM sodium citrate, pH 5.85, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 115975 / Num. obs: 115975 / % possible obs: 98.5 % / Observed criterion σ(I): -1 / Rmerge(I) obs: 0.138 / Net I/σ(I): 8.16
Reflection shellResolution: 3.3→3.42 Å / % possible all: 93.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IW7

1iw7


Resolution: 3.3→30 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 CRYSTALS HAVE THE SYMMETRY OF SPACE GROUP P32 WITH PERFECT (50%) HEMIHEDRAL ...Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (-H,-K,L) AND THE TWINNING FRACTION IS 0.5. THE CRYSTALS HAVE THE SYMMETRY OF SPACE GROUP P32 WITH PERFECT (50%) HEMIHEDRAL TWINNING AND TWINNING OPERATOR (-H, -K, L), LEADING TO APPARENT HEXAGONAL (P6/M) INTENSITY SYMMETRY. PROCESSING AND SCALING WERE CARRIED OUT IN P65 FOLLOWED BY EXPANSION TO P32 FOR STRUCTURE SOLUTION AND REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.32 1953 -random
Rwork0.282 ---
all-196849 --
obs-196849 84.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53956 0 6 0 53962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d60
X-RAY DIFFRACTIONc_improper_angle_d3

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