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- PDB-3dxj: Crystal structure of thermus thermophilus rna polymerase holoenzy... -

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Basic information

Entry
Database: PDB / ID: 3dxj
TitleCrystal structure of thermus thermophilus rna polymerase holoenzyme in complex with the antibiotic myxopyronin
Components
  • (BACTERIAL RNA POLYMERASE ...) x 3
  • DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L
  • RNA polymerase pricipal sigma factor (RpoD); CHAIN F, P
KeywordsTRANSCRIPTION / TRANSFERASE / RNA POLYMERASE / RNAP / DRUG COMPLEX / INHIBITOR / corallopyronin / ripostatin / HOLOENZYME / CRYSTALLOGRAPHY / TWINNING / HEMIHEDRAL / DNA-directed RNA polymerase / Nucleotidyltransferase / DNA-binding / Sigma factor / Transcription regulation
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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / 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 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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
Similarity search - Domain/homology
Chem-NE6 / PHOSPHATE ION / 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 HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 3 Å
AuthorsDas, K. / Arnold, E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: The RNA polymerase "switch region" is a target for inhibitors.
Authors: Mukhopadhyay, J. / Das, K. / Ismail, S. / Koppstein, D. / Jang, M. / Hudson, B. / Sarafianos, S. / Tuske, S. / Patel, J. / Jansen, R. / Irschik, H. / Arnold, E. / Ebright, R.H.
History
DepositionJul 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / 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 / _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_ref_seq_dif.details / _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 subunit alpha; CHAIN A, B, K, L
B: DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L
C: BACTERIAL RNA POLYMERASE BETA SUBUNIT; CHAIN C, M
D: BACTERIAL RNA POLYMERASE BETA-PRIME SUBUNIT; CHAIN D, N
E: BACTERIAL RNA POLYMERASE OMEGA SUBUNIT; CHAIN E, O
F: RNA polymerase pricipal sigma factor (RpoD); CHAIN F, P
K: DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L
L: DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L
M: BACTERIAL RNA POLYMERASE BETA SUBUNIT; CHAIN C, M
N: BACTERIAL RNA POLYMERASE BETA-PRIME SUBUNIT; CHAIN D, N
O: BACTERIAL RNA POLYMERASE OMEGA SUBUNIT; CHAIN E, O
P: RNA polymerase pricipal sigma factor (RpoD); CHAIN F, P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)855,04526
Polymers853,33112
Non-polymers1,71414
Water54030
1
A: DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L
B: DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L
C: BACTERIAL RNA POLYMERASE BETA SUBUNIT; CHAIN C, M
D: BACTERIAL RNA POLYMERASE BETA-PRIME SUBUNIT; CHAIN D, N
E: BACTERIAL RNA POLYMERASE OMEGA SUBUNIT; CHAIN E, O
F: RNA polymerase pricipal sigma factor (RpoD); CHAIN F, P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,68915
Polymers426,6666
Non-polymers1,0239
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42120 Å2
ΔGint-213 kcal/mol
Surface area158080 Å2
MethodPISA
2
K: DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L
L: DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L
M: BACTERIAL RNA POLYMERASE BETA SUBUNIT; CHAIN C, M
N: BACTERIAL RNA POLYMERASE BETA-PRIME SUBUNIT; CHAIN D, N
O: BACTERIAL RNA POLYMERASE OMEGA SUBUNIT; CHAIN E, O
P: RNA polymerase pricipal sigma factor (RpoD); CHAIN F, P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,35611
Polymers426,6666
Non-polymers6915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41900 Å2
ΔGint-180 kcal/mol
Surface area157750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.090, 235.090, 250.880
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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Protein , 2 types, 6 molecules ABKLFP

#1: Protein
DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L


Mass: 35056.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHR6, DNA-directed RNA polymerase
#5: Protein RNA polymerase pricipal sigma factor (RpoD); CHAIN F, P


Mass: 48598.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SKW1, DNA-directed RNA polymerase

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BACTERIAL RNA POLYMERASE ... , 3 types, 6 molecules CMDNEO

#2: Protein BACTERIAL RNA POLYMERASE BETA SUBUNIT; CHAIN C, M


Mass: 125436.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q8RQE9, DNA-directed RNA polymerase
#3: Protein BACTERIAL RNA POLYMERASE BETA-PRIME SUBUNIT; CHAIN D, N


Mass: 170997.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q8RQE8, DNA-directed RNA polymerase
#4: Protein BACTERIAL RNA POLYMERASE OMEGA SUBUNIT; CHAIN E, O


Mass: 11521.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q8RQE7, DNA-directed RNA polymerase

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Non-polymers , 6 types, 44 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#10: Chemical ChemComp-NE6 / methyl [(1E,5R)-5-{(3S)-3-[(2E,4E)-2,5-dimethylocta-2,4-dienoyl]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hexylidene]carbamate


Mass: 417.495 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H31NO6
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 4.69 Å3/Da / Density % sol: 73.78 %
Crystal growTemperature: 298 K / pH: 5.85
Details: MES, MAGNESIUM FORMATE, PEG 8000, SPERMINE, pH 5.85, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 150814 / % possible obs: 96 % / Observed criterion σ(I): -1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.8
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.33 / % possible all: 77.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 1IW7

1iw7


Resolution: 3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: THE FRIEDEL PAIRS WERE USED FOR PHASING; DIFFRACTION DATA PROCESSED IN SPECE GROUP P 65 AND EXTENDED TO P3(2); MEROHEDRAL TWINNING (-H,-K,L) WITH TWINNING FRACTION 0.5; THE STRUCTURE REFINED ...Details: THE FRIEDEL PAIRS WERE USED FOR PHASING; DIFFRACTION DATA PROCESSED IN SPECE GROUP P 65 AND EXTENDED TO P3(2); MEROHEDRAL TWINNING (-H,-K,L) WITH TWINNING FRACTION 0.5; THE STRUCTURE REFINED USING _TWIN ROUTINES IN CNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2351 -RANDOM
Rwork0.235 ---
obs0.235 298910 96.3 %-
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56018 0 77 54 56149
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.57
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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: 3→3.14 Å /
RfactorNum. reflection
Rfree0.365 308
Rwork0.339 -

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