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- PDB-6cce: Crystal structure of a Mycobacterium smegmatis RNA polymerase tra... -

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Basic information

Entry
Database: PDB / ID: 6cce
TitleCrystal structure of a Mycobacterium smegmatis RNA polymerase transcription initiation complex with inhibitor Kanglemycin A
Components
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • DNA (57-MER)
  • RNA polymerase sigma factor SigA
  • RNA polymerase-binding protein RbpA
  • poly(UNK)
Keywordstranscription/dna/antibiotic / RNA polymerase antibiotic complex inhibitor tuberculosis / TRANSCRIPTION / transcription-antibiotic complex / transcription-dna-antibiotic complex
Function / homology
Function and homology information


bacterial-type RNA polymerase core enzyme 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 / response to antibiotic / DNA-templated transcription ...bacterial-type RNA polymerase core enzyme 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 / response to antibiotic / DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
RNA polymerase-binding protein RbpA / RbpA superfamily / RNA polymerase-binding protein / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Sigma-70 factors family signature 1. / 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 ...RNA polymerase-binding protein RbpA / RbpA superfamily / RNA polymerase-binding protein / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Sigma-70 factors family signature 1. / 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 / 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 / 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 / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Kanglemycin A / DNA / DNA (> 10) / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit alpha / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / RNA polymerase-binding protein RbpA / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
Mycobacterium smegmatis str. MC2 155 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsLilic, M. / Darst, S.A. / Campbell, E.A.
CitationJournal: Nat Commun / Year: 2018
Title: Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism.
Authors: Peek, J. / Lilic, M. / Montiel, D. / Milshteyn, A. / Woodworth, I. / Biggins, J.B. / Ternei, M.A. / Calle, P.Y. / Danziger, M. / Warrier, T. / Saito, K. / Braffman, N. / Fay, A. / Glickman, ...Authors: Peek, J. / Lilic, M. / Montiel, D. / Milshteyn, A. / Woodworth, I. / Biggins, J.B. / Ternei, M.A. / Calle, P.Y. / Danziger, M. / Warrier, T. / Saito, K. / Braffman, N. / Fay, A. / Glickman, M.S. / Darst, S.A. / Campbell, E.A. / Brady, S.F.
History
DepositionFeb 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: RNA polymerase-binding protein RbpA
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
O: DNA (57-MER)
G: poly(UNK)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)448,86224
Polymers446,6849
Non-polymers2,17815
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48440 Å2
ΔGint-340 kcal/mol
Surface area139560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.564, 161.583, 135.141
Angle α, β, γ (deg.)90.00, 110.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules JF

#1: Protein RNA polymerase-binding protein RbpA


Mass: 13078.731 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: rbpA, MSMEG_3858, MSMEI_3768 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QZ11
#6: Protein RNA polymerase sigma factor SigA


Mass: 51573.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: sigA, MSMEG_2758 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QW02

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE

#2: Protein DNA-directed RNA polymerase subunit alpha / Polymerase / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 37959.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL8, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta / Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 128680.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: P60281, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit beta' / Polymerase / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 146712.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS66, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase subunit omega / Polymerase / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 11544.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QWT1, DNA-directed RNA polymerase

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DNA chain / Protein/peptide , 2 types, 2 molecules OG

#7: DNA chain DNA (57-MER)


Mass: 17540.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: Protein/peptide poly(UNK)


Mass: 1635.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 15 molecules

#9: Chemical ChemComp-KNG / Kanglemycin A / 4-{(1S)-1-[(1S,2S,12S,16S,17R,18S,19R,20R,21S,22R,23S,24E)-21-(acetyloxy)-23-[(2,6-dideoxy-3,4-O-methylidene-beta-D-ribo-hexopyranosyl)oxy]-1,5,6,9,17,19-hexahydroxy-2,4,12,18,20,22-hexamethyl-11-oxo-1,2-dihydro-2,7-(epoxypentadec[1]enoimino)naphtho[2,1-b]furan-16-yl]ethoxy}-3,3-dimethyl-4-oxobutanoic acid


Mass: 986.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H67NO19
#10: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Zn
#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#13: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#14: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2

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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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris, pH 6.0, 0.2 M LiSO4, 16% (w/v) polyetheylene glycol 3350, 2.5% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.91806 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91806 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 99721 / % possible obs: 99.76 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.0637 / Rrim(I) all: 0.157 / Net I/σ(I): 8.42
Reflection shellResolution: 3.05→3.16 Å / Rmerge(I) obs: 2.227 / CC1/2: 0.31 / Rpim(I) all: 1.032 / Rrim(I) all: 2.462

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TW1

5tw1


Resolution: 3.05→49.549 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 1810 1.82 %
Rwork0.2345 --
obs0.235 99564 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→49.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24063 1161 133 0 25357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225867
X-RAY DIFFRACTIONf_angle_d0.48535342
X-RAY DIFFRACTIONf_dihedral_angle_d15.48115535
X-RAY DIFFRACTIONf_chiral_restr0.0384095
X-RAY DIFFRACTIONf_plane_restr0.0034441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.13250.45681420.44417338X-RAY DIFFRACTION98
3.1325-3.22460.36871340.35957521X-RAY DIFFRACTION100
3.2246-3.32870.36831420.31957463X-RAY DIFFRACTION100
3.3287-3.44760.35851450.30927551X-RAY DIFFRACTION100
3.4476-3.58560.35861340.31277507X-RAY DIFFRACTION100
3.5856-3.74870.29491380.2767542X-RAY DIFFRACTION100
3.7487-3.94630.2941410.25547493X-RAY DIFFRACTION100
3.9463-4.19340.27271380.22887532X-RAY DIFFRACTION100
4.1934-4.5170.22871380.20787544X-RAY DIFFRACTION100
4.517-4.97120.22571360.20357497X-RAY DIFFRACTION100
4.9712-5.68960.2591380.22137565X-RAY DIFFRACTION100
5.6896-7.16490.2741400.23417564X-RAY DIFFRACTION100
7.1649-49.55580.20711440.18377637X-RAY DIFFRACTION100

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