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- PDB-1zyr: Structure of Thermus thermophilus RNA polymerase holoenzyme in co... -

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Basic information

Entry
Database: PDB / ID: 1zyr
TitleStructure of Thermus thermophilus RNA polymerase holoenzyme in complex with the antibiotic streptolydigin
Components(DNA-directed RNA polymerase ...Polymerase) x 5
KeywordsTRANSCRIPTION / TRANSFERASE / RNA polymerase / streptolydigin / holoenzyme
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
STREPTOLYDIGIN / 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 Å
AuthorsTuske, S. / Sarafianos, S.G. / Wang, X. / Hudson, B. / Sineva, E. / Mukhopadhyay, J. / Birktoft, J.J. / Leroy, O. / Ismail, S. / Clark, A.D. ...Tuske, S. / Sarafianos, S.G. / Wang, X. / Hudson, B. / Sineva, E. / Mukhopadhyay, J. / Birktoft, J.J. / Leroy, O. / Ismail, S. / Clark, 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, A.D. / Dharia, C. / Napoli, A. / Laptenko, O. / Lee, J. ...Authors: Tuske, S. / Sarafianos, S.G. / Wang, X. / Hudson, B. / Sineva, E. / Mukhopadhyay, J. / Birktoft, J.J. / Leroy, O. / Ismail, S. / Clark, A.D. / Dharia, C. / Napoli, A. / Laptenko, O. / Lee, J. / Borukhov, S. / Ebright, R.H. / Arnold, E.
History
DepositionJun 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 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_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_conn.ptnr2_label_seq_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

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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 subunit beta' chain
E: DNA-directed RNA polymerase omega chain
F: DNA-directed RNA polymerase sigma chain
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 subunit beta' chain
O: DNA-directed RNA polymerase omega chain
P: DNA-directed RNA polymerase sigma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)854,78320
Polymers853,27112
Non-polymers1,5128
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 subunit beta' chain
E: DNA-directed RNA polymerase omega chain
F: DNA-directed RNA polymerase sigma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,39110
Polymers426,6356
Non-polymers7564
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44530 Å2
ΔGint-228 kcal/mol
Surface area148680 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 subunit beta' chain
O: DNA-directed RNA polymerase omega chain
P: DNA-directed RNA polymerase sigma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,39110
Polymers426,6356
Non-polymers7564
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43860 Å2
ΔGint-206 kcal/mol
Surface area149150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)237.000, 237.000, 250.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Cell settingtrigonal
Space group name H-MP32

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Components

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DNA-directed RNA polymerase ... , 5 types, 12 molecules ABKLCMDNEOFP

#1: Protein
DNA-directed RNA polymerase alpha chain / E.C.2.7.7.6 / RNAP alpha subunit / Transcriptase alpha chain / RNA polymerase alpha subunit


Mass: 35056.164 Da / Num. of mol.: 4 / Fragment: subumit alpha / 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 / E.C.2.7.7.6 / RNAP beta subunit / Transcriptase beta chain / RNA polymerase beta subunit


Mass: 125436.539 Da / Num. of mol.: 2 / Fragment: subunit beta / 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 subunit beta' chain / Polymerase / E.C.2.7.7.6 / RNAP beta


Mass: 170997.391 Da / Num. of mol.: 2 / Fragment: subunit beta-prime / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q8RQE8, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase omega chain / RNAP omega subunit / Transcriptase omega chain / RNA polymerase omega subunit


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


Mass: 48568.008 Da / Num. of mol.: 2 / Fragment: subunit sigma / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SKW1

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Non-polymers , 3 types, 8 molecules

#6: Chemical ChemComp-STD / STREPTOLYDIGIN / 2-PYRROLIDINEACETAMIDE / PORTAMYCIN / Streptolydigin


Mass: 600.700 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H44N2O9 / Comment: antibiotic*YM
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#8: 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

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Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.85
Details: 33 mM Magnesium formate over a reservoir of 33 mM Magnesium format and 30 mM 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 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 139391 / Num. obs: 139391 / Observed criterion σ(I): -1 / Redundancy: 6.1 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 10.7
Reflection shellResolution: 3→3.11 Å

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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→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2815 2422 -
Rwork0.2612 --
all-139391 -
obs-139391 77.9 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.141 Å2-7.657 Å20 Å2
2--0.176 Å20 Å2
3----0.317 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a1 Å0.93 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53956 0 93 0 54049
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d60
X-RAY DIFFRACTIONc_improper_angle_d3
X-RAY DIFFRACTIONc_mcbond_it1.1831.5
X-RAY DIFFRACTIONc_mcangle_it2.1062
X-RAY DIFFRACTIONc_scbond_it1.2752
X-RAY DIFFRACTIONc_scangle_it2.1452.5

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