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- EMDB-23210: Clostridioides difficile RNAP with fidaxomicin -

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Basic information

Entry
Database: EMDB / ID: EMD-23210
TitleClostridioides difficile RNAP with fidaxomicin
Map data
Sample
  • Complex: Clostridioides difficile RNA polymerase in complex with fidaxomicin
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Protein or peptide: RNA polymerase sigma factor SigA
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: Fidaxomicin
  • Ligand: water
Keywordsfidaxomicin / Clostridioides difficile RNA polymerase / TRANSCRIPTION / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


DNA-templated transcription initiation => GO:0006352 / sigma factor activity / DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...DNA-templated transcription initiation => GO:0006352 / sigma factor activity / DNA-directed RNA polymerase complex / 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 / cytoplasm
Similarity search - Function
RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / 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 ...RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / 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 / 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 / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
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 speciesClostridia bacterium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsBoyaci H / Campbell EA
Funding support1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
CitationJournal: Nature / Year: 2022
Title: Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile.
Authors: Xinyun Cao / Hande Boyaci / James Chen / Yu Bao / Robert Landick / Elizabeth A Campbell /
Abstract: Fidaxomicin (Fdx) is widely used to treat Clostridioides difficile (Cdiff) infections, but the molecular basis of its narrow-spectrum activity in the human gut microbiome remains unknown. Cdiff ...Fidaxomicin (Fdx) is widely used to treat Clostridioides difficile (Cdiff) infections, but the molecular basis of its narrow-spectrum activity in the human gut microbiome remains unknown. Cdiff infections are a leading cause of nosocomial deaths. Fidaxomicin, which inhibits RNA polymerase, targets Cdiff with minimal effects on gut commensals, reducing recurrence of Cdiff infection. Here we present the cryo-electron microscopy structure of Cdiff RNA polymerase in complex with fidaxomicin and identify a crucial fidaxomicin-binding determinant of Cdiff RNA polymerase that is absent in most gut microbiota such as Proteobacteria and Bacteroidetes. By combining structural, biochemical, genetic and bioinformatic analyses, we establish that a single residue in Cdiff RNA polymerase is a sensitizing element for fidaxomicin narrow-spectrum activity. Our results provide a blueprint for targeted drug design against an important human pathogen.
History
DepositionDec 28, 2020-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7l7b
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7l7b
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23210.png

Downloads & links

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Map

FileDownload / File: emd_23210.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 277.248 Å		1.08 Å/pix.
x 256 pix.
= 277.248 Å		1.08 Å/pix.
x 256 pix.
= 277.248 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-2.2985058 - 4.1156583
Average (Standard dev.)0.020491466 (±0.12041223)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.248 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0831.0831.083
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z277.248277.248277.248
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.2994.1160.020

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Supplemental data

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Sample components

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Entire : Clostridioides difficile RNA polymerase in complex with fidaxomicin

EntireName: Clostridioides difficile RNA polymerase in complex with fidaxomicin
Components
  • Complex: Clostridioides difficile RNA polymerase in complex with fidaxomicin
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Protein or peptide: RNA polymerase sigma factor SigA
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: Fidaxomicin
  • Ligand: water

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Supramolecule #1: Clostridioides difficile RNA polymerase in complex with fidaxomicin

SupramoleculeName: Clostridioides difficile RNA polymerase in complex with fidaxomicin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Clostridia bacterium (bacteria)

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Macromolecule #1: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Clostridia bacterium (bacteria)
Molecular weightTheoretical: 34.958883 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIEIEKPKVD IVELSEDYRY GKFVIEPLER GYGITIGNAL RRILLSSLPG VAVNAIKIDG VLHEFSTIPG VKEDVTEIIL TLKELSATI DGEGSRTLKI EAQGPCSITG ADIICPPDVE ILSKDLAIAT LDDNAKLNME IFVDKGRGYV SAEENKTENV P IGVLPVDS ...String:
MIEIEKPKVD IVELSEDYRY GKFVIEPLER GYGITIGNAL RRILLSSLPG VAVNAIKIDG VLHEFSTIPG VKEDVTEIIL TLKELSATI DGEGSRTLKI EAQGPCSITG ADIICPPDVE ILSKDLAIAT LDDNAKLNME IFVDKGRGYV SAEENKTENV P IGVLPVDS IYTPVEKVSY HVENTRVGQK TDYDKLVLEV WTNGSINPQE GISLAAKVLV EHLNLFIDLT EHVSSVEIMV EK EEDQKEK VLEMTIEELD LSVRSYNCLK RAGINTVEEL ANKSEDDMMK VRNLGKKSLE EVIQKLEELG LGLKPSEE

UniProtKB: DNA-directed RNA polymerase subunit alpha

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Macromolecule #2: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Clostridia bacterium (bacteria)
Molecular weightTheoretical: 142.367359 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWSHPQFEKG GGSGGGSGGS AWSHPQFEKP HPVTIGKRTR MSFSKIKEIA DVPNLIEIQV DSYEWFLKEG LKEVFDDISP IEDYTGNLI LEFVDYSLDD KPKYDIEECK ERDATYCAPL KVKVRLINKE TGEIKEQEVF MGDFPLMTER GTFVINGAER V IVSQLVRS ...String:
MWSHPQFEKG GGSGGGSGGS AWSHPQFEKP HPVTIGKRTR MSFSKIKEIA DVPNLIEIQV DSYEWFLKEG LKEVFDDISP IEDYTGNLI LEFVDYSLDD KPKYDIEECK ERDATYCAPL KVKVRLINKE TGEIKEQEVF MGDFPLMTER GTFVINGAER V IVSQLVRS PGVYYAEERD KTGKRLISST VIPNRGAWLE YETDSNDVIS VRVDRTRKQP VTVLLRALGI GTDAEIIDLL GE DERLSAT LEKDNTKTVE EGLVEIYKKL RPGEPPTVES ASSLLNALFF DPKRYDLAKV GRYKFNKKLA LCYRIMNKIS AED IINPET GEVFVKAGEK ISYDLAKAIQ NAGINVVNLL MDDDKKVRVI GNNFVDIKSH IDFDIDDLNI KEKVHYPTLK EILD GYSDE EEIKEAIKSR IKELIPKHIL LDDIIASISY EFNIFYNIGN IDDIDHLGNR RIRSVGELLQ NQVRIGLSRM ERVIK ERMT VQDMEAITPQ ALVNIRPVSA AIKEFFGSSQ LSQFMDQTNP LSELTHKRRL SALGPGGLSR ERAGFEVRDV HHSHYG RMC PIETPEGPNI GLINSLGTYA KINEFGFIES PYRKFDKETS TVTDEIHYLT ADEEDLFVRA QANEPLTEDG KFVNHRV VC RTVNGAVEMV PESRVDYMDI SPKQVVSVAT AMIPFLENDD ANRALMGANM QRQAVPLVRR EAPIIGTGIE YRAAKDSG A VVVARNSGIA ERVTADEIII KREDGNRDRY NLLKFKRSNS GTCINQTPII NKGDQIIKGD VIADGPATDL GEVALGRNC LIAFMTWEGY NYEDAILINE RLVKEDRLST IHIEEYECEA RDTKLGPEEI TRDIPNVGDS AIKNLDDRGI IRIGAEVDSG DILVGKVTP KGETELTAEE RLLRAIFGEK AREVRDTSLK VPHGESGIIV DVKVFTRENG DDLSPGVNEL VRCYIAKKRK I KVGDKMAG RHGNKGVISR VLPEEDMPFM ENGTPLDIIL NPQGIPSRMN IGQVLEVHLG LAAKTLGWYV ATSVFDGANE YD IMDALEE AGYPRDGKLT LYDGRTGESF DNRITVGYMY YLKLHHLVDE KLHARSTGPY SLVTQQPLGG KAQFGGQRFG EME VWALEA YGAAHILQEI LTVKSDDVVG RVRTYEAIVK GENIPEPGIP ESFKVLIKEL QSLCLDVKVL TDEDQEIEVR ESVD EDDTI GEFELDVVNH MGEVEESNII EEIEDDFAEN AEDEDIENLE EFTEDDLFEE EIDFDSDDFD M

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #3: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Clostridia bacterium (bacteria)
Molecular weightTheoretical: 129.916414 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFELNNFESI KIALASPEKI RQWSRGEVKK PETINYRTLK PEKDGLFCER IFGPQKDWEC HCGKYRRVRY KGVVCDRCGV EVTKSKVRR ERMGHIELAA PMSHIWYFKG IPSRMGLLLD MSPRSLEKIL YFASYVVVDP GETGLNEKQL LTEKEYRTAL E KYGYTFTV ...String:
MFELNNFESI KIALASPEKI RQWSRGEVKK PETINYRTLK PEKDGLFCER IFGPQKDWEC HCGKYRRVRY KGVVCDRCGV EVTKSKVRR ERMGHIELAA PMSHIWYFKG IPSRMGLLLD MSPRSLEKIL YFASYVVVDP GETGLNEKQL LTEKEYRTAL E KYGYTFTV GMGAEAVKTL LQNIDLEQQS KDLRAELKDS TGQKKVRTIR RLEVVEAFKK SGNKPEWMIL DAIPVIPPDL RP MVQLDGG RFATSDLNDL YRRVINRNNR LKRLLELGAP DIIVRNEKRM LQEAVDALID NGRRGRPVTG PGNRPLKSLS DML KGKQGR FRQNLLGKRV DYSGRSVIVV GPELKFYQCG LPKKMALELF KPFVMDKLVK EGYAHNIKSA KSIVEKVKPE VWDV LEDVI KSHPVLLNRA PTLHRLGIQA FEPILVEGKA IKLHPLVCTA YNADFDGDQM AVHVPLSVEA QAEARFLMLS VNNIL APKD GSPITTPSQD MVLGCYYLTI EAQDGAKGTG MVFKDFNELL LAYYNKSVHL HALVKLKVTL EDGRSSLVES TVGRFI FNE NIPQDLGFVD RKENPFALEV DFLADKKSLG KIIDKCFRKH GNTETAELLD YIKALGFKYS TLGGITVAVD DMSVPEE KK VFIAEAEAKV DKYEKAYRRG LISDEERYEK VIETWTETTD KVTDALMGGL DRLNNIYIMA HSGARGSKNQ IRQLAGMR G LMANASGKTV EIPVKSNFRE GLSVLEYFTS SHGARKGLAD TAIRTAESGY LTRRLVDVSQ DVIVREIDCG TEDTTEIYA IKEGNEVIEE IYDRIVGRYT IDPILNPETG EVIVEADSMI QEDEAETIVA LGIEKIRIRT VLNCKTNHGV CSKCYGRNLA TGKEVNIGE AVGIIAAQSI GEPGTQLTMR TFHTGGVAGA DITQGLPRVE ELFEARKPKG LAVITEVSGR VEIDETGKRK E VNVIPEEG ETQTYVIPYG SRLKVKQGQM LEAGDPLTQG FINPHDIVRV NGVKGVQEYI VKEVQRVYRL QGVDVNDKHI EV IVRQMLS KVKVEDPGDT DLLPGGYEDV LTFNECNKDA IDKGLRPAVA KRVLLGITKA SLATDSFLSA ASFQETTRVL TEA AIKGKE DHLIGLKENV ILGKLIPAGT GMKKYRNIAV EKIED

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #4: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Clostridia bacterium (bacteria)
Molecular weightTheoretical: 10.214526 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLKPSINEVL EKIDNRYYLV GTVSKRARKL IDGEEPYVSN KTKEKPVCVA TKEVASGKIT YRLLTEEEIE IEEARHHAEQ HQQISEEE

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #5: RNA polymerase sigma factor SigA

MacromoleculeName: RNA polymerase sigma factor SigA / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridia bacterium (bacteria)
Molecular weightTheoretical: 44.476625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LSVENKSNKK ELKKVTAKTL IEKGKKQGSL TLAEIMEAFS ETELDKDQVE NLYETLGNLG IEITETKNYK ADIDFSVADD DLSIGHLDE DAEAISHDDS SAIEIETVDL SLPKGISIDD PVRMYLKEIG KIPLLKPHEE VEFARRMHEG DEIAKQRLVE A NLRLVVSI ...String:
LSVENKSNKK ELKKVTAKTL IEKGKKQGSL TLAEIMEAFS ETELDKDQVE NLYETLGNLG IEITETKNYK ADIDFSVADD DLSIGHLDE DAEAISHDDS SAIEIETVDL SLPKGISIDD PVRMYLKEIG KIPLLKPHEE VEFARRMHEG DEIAKQRLVE A NLRLVVSI AKRYVGRGML FLDLIQEGNL GLIKAVEKFD YTKGYKFSTY ATWWIRQAIT RAIADQARTI RIPVHMVETI NK LIRVSRQ LLQELGRDPK PEEIAKEMEM TEDKVREIMK IAQDPVSLET PIGEEEDSHL GDFIPDDDAP APAEAAAYSL LKE QIEDVL GSLNDREQKV LKLRFGLEDG RARTLEEVGK EFDVTRERIR QIEAKALRKL RHPSRSKKLR DYLD

UniProtKB: RNA polymerase sigma factor SigA

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: Fidaxomicin

MacromoleculeName: Fidaxomicin / type: ligand / ID: 8 / Number of copies: 1 / Formula: FI8
Molecular weightTheoretical: 1.058039 KDa
Chemical component information

ChemComp-FI8:
Fidaxomicin / antibiotic*YM

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 31 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 182390
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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