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- PDB-5uh6: Crystal structure of Mycobacterium tuberculosis transcription ini... -

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Basic information

Entry
Database: PDB / ID: 5uh6
TitleCrystal structure of Mycobacterium tuberculosis transcription initiation complex containing 2ntRNA in complex with Rifampin
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • DNA (5'-D(*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*G)-3')
  • DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*G)-3')
  • RNA (5'-R(*GP*A)-3')
  • RNA polymerase sigma factor SigA
Keywordstranscription/dna/rna/antibiotic / RNA polymerase complex / transcription / DNA / RNA / TRANSCRIPTION-DNA-RNA complex / transcription-dna-rna-antibiotic complex
Function / homology
Function and homology information


response to water / Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase ...response to water / Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / response to antibiotic / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / Sigma-70 factors family signature 1. / 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 Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / Sigma-70 factors family signature 1. / 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 / Beta Complex / 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 / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RIFAMPICIN / DNA / DNA (> 10) / RNA / 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 speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.837 Å
AuthorsLin, W. / Das, K. / Feng, Y. / Ebright, R.H.
CitationJournal: Mol. Cell / Year: 2017
Title: Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition.
Authors: Lin, W. / Mandal, S. / Degen, D. / Liu, Y. / Ebright, Y.W. / Li, S. / Feng, Y. / Zhang, Y. / Mandal, S. / Jiang, Y. / Liu, S. / Gigliotti, M. / Talaue, M. / Connell, N. / Das, K. / Arnold, E. / Ebright, R.H.
History
DepositionJan 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 3, 2017Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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: RNA polymerase sigma factor SigA
H: DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*G)-3')
G: DNA (5'-D(*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*G)-3')
I: RNA (5'-R(*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)435,87413
Polymers434,8969
Non-polymers9784
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51080 Å2
ΔGint-235 kcal/mol
Surface area140000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.236, 164.889, 199.969
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 37745.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: rpoA, Rv3457c, MTCY13E12.10c
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WGZ1, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 130018.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: rpoB, Rv0667, MTCI376.08c
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WGY9, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 146968.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: rpoC, Rv0668, MTCI376.07c
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WGY7, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 11851.140 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: rpoZ, Rv1390, MTCY21B4.07
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WGY5, DNA-directed RNA polymerase

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DNA chain , 2 types, 2 molecules HG

#6: DNA chain DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*G)-3')


Mass: 7160.632 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
#7: DNA chain DNA (5'-D(*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*G)-3')


Mass: 4899.180 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)

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Protein / RNA chain , 2 types, 2 molecules FI

#5: Protein RNA polymerase sigma factor SigA / Sigma-A


Mass: 57877.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: sigA, mysA, rpoD, rpoV, Rv2703, MTCY05A6.24
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WGI1
#8: RNA chain RNA (5'-R(*GP*A)-3')


Mass: 629.454 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)

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Non-polymers , 3 types, 4 molecules

#9: Chemical ChemComp-RFP / RIFAMPICIN


Mass: 822.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H58N4O12
#10: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#11: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 50 mM Tris-HCl, pH 8.2, 200 mM KCl, 50 mM MgCl2, and 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.929 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.929 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 47440 / % possible obs: 97.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.046 / Rrim(I) all: 0.142 / Χ2: 1.11 / Net I/σ(I): 6.8 / Num. measured all: 355801
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.8-3.944.30.844040.4320.4010.9010.84492.6
3.94-4.094.90.72245310.5290.3350.80.82194.4
4.09-4.285.60.61945890.710.2690.6770.88595.8
4.28-4.56.20.50846560.8280.2090.5510.94596.8
4.5-4.796.90.42347320.8460.1650.4550.98598.4
4.79-5.167.60.39647940.8790.1470.4231.02599.3
5.16-5.678.50.36648250.9160.1280.3881.03799.6
5.67-6.499.40.30848700.9380.1010.3241.10199.9
6.49-8.1810.30.16549250.9740.0520.1731.437100
8.18-5010.60.07851140.9590.0240.0821.3599.7

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Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
RefinementResolution: 3.837→50.087 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 21.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 1996 5.02 %
Rwork0.2117 --
obs0.2143 39783 80.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 244.8 Å2 / Biso mean: 60.2698 Å2 / Biso min: 2.44 Å2
Refinement stepCycle: final / Resolution: 3.837→50.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25203 821 104 0 26128
Biso mean--34.41 --
Num. residues----3281

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