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- EMDB-38196: Cryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-38196
TitleCryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex
Map data
Sample
  • Complex: Cryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex
    • 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
    • Protein or peptide: Gene 33 protein
    • Protein or peptide: DNA-directed RNA polymerase subunit delta
    • Protein or peptide: DNA-directed RNA polymerase subunit epsilon
Keywordsbacterial / phage / complex / TRANSCRIPTION
Function / homology
Function and homology information


nucleoid / sigma factor activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : ...nucleoid / sigma factor activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
RNA polymerase epsilon subunit / RNA polymerase epsilon subunit / DNA-directed RNA polymerase subunit delta / DNA-directed RNA polymerase subunit delta, N-terminal domain superfamily / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 ...RNA polymerase epsilon subunit / RNA polymerase epsilon subunit / DNA-directed RNA polymerase subunit delta / DNA-directed RNA polymerase subunit delta, N-terminal domain superfamily / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / 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 / 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 / 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 Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit epsilon / DNA-directed RNA polymerase subunit omega / RNA polymerase sigma factor SigA / Gene 33 protein / DNA-directed RNA polymerase subunit delta / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesBacillus (Bacillus rRNA group 1) / Bacillus phage SPO1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsChen M / Jin Q / Yuan S / Liu B
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270151 China
National Natural Science Foundation of China (NSFC)32270172 China
CitationJournal: To Be Published
Title: A phage encoded sigA-dependent transcription inhibitor also attacks host HelD-mediated defence system
Authors: Chen M / Jin Q / Zhang K / Wang Y / Chen H / Yu Z / Matthews S / Yuan S / Liu B
History
DepositionDec 2, 2023-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38196.png

Downloads & links

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Map

FileDownload / File: emd_38196.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.195
Minimum - Maximum-1.3992695 - 1.8272552
Average (Standard dev.)0.0000773082 (±0.037197117)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 380.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38196_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38196_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex

EntireName: Cryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex
Components
  • Complex: Cryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex
    • 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
    • Protein or peptide: Gene 33 protein
    • Protein or peptide: DNA-directed RNA polymerase subunit delta
    • Protein or peptide: DNA-directed RNA polymerase subunit epsilon

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Supramolecule #1: Cryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex

SupramoleculeName: Cryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)

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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
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)
Molecular weightTheoretical: 34.842387 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MIEIEKPKIE TVEISDDAKF GKFVVEPLER GYGTTLGNSL RRILLSSLPG AAVTSIQIDG VLHEFSTIEG VVEDVTTIIL HIKKLALKI YSDEEKTLEI DVQGEGTVTA ADITHDSDVE ILNPDLHIAT LGENASFRVR LTAQRGRGYT PADANKRDDQ P IGVIPIDS ...String:
MIEIEKPKIE TVEISDDAKF GKFVVEPLER GYGTTLGNSL RRILLSSLPG AAVTSIQIDG VLHEFSTIEG VVEDVTTIIL HIKKLALKI YSDEEKTLEI DVQGEGTVTA ADITHDSDVE ILNPDLHIAT LGENASFRVR LTAQRGRGYT PADANKRDDQ P IGVIPIDS IYTPVSRVSY QVENTRVGQV ANYDKLTLDV WTDGSTGPKE AIALGSKILT EHLNIFVGLT DEAQHAEIMV EK EEDQKEK VLEMTIEELD LSVRSYNCLK RAGINTVQEL ANKTEEDMMK VRNLGRKSLE EVKAKLEELG LGLRKDD

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
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)
Molecular weightTheoretical: 133.847938 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MTGQLVQYGR HRQRRSYARI SEVLELPNLI EIQTSSYQWF LDEGLREMFQ DISPIEDFTG NLSLEFIDYS LGEPKYPVEE SKERDVTYS APLRVKVRLI NKETGEVKDQ DVFMGDFPIM TDTGTFIING AERVIVSQLV RSPSVYFSGK VDKNGKKGFT A TVIPNRGA ...String:
MTGQLVQYGR HRQRRSYARI SEVLELPNLI EIQTSSYQWF LDEGLREMFQ DISPIEDFTG NLSLEFIDYS LGEPKYPVEE SKERDVTYS APLRVKVRLI NKETGEVKDQ DVFMGDFPIM TDTGTFIING AERVIVSQLV RSPSVYFSGK VDKNGKKGFT A TVIPNRGA WLEYETDAKD VVYVRIDRTR KLPVTVLLRA LGFGSDQEIL DLIGENEYLR NTLDKDNTEN SDKALLEIYE RL RPGEPPT VENAKSLLDS RFFDPKRYDL ANVGRYKINK KLHIKNRLFN QRLAETLVDP ETGEILAEKG QILDRRTLDK VLP YLENGI GFRKLYPNGG VVEDEVTLQS IKIFAPTDQE GEQVINVIGN AYIEEEIKNI TPADIISSIS YFFNLLHGVG DTDD IDHLG NRRLRSVGEL LQNQFRIGLS RMERVVRERM SIQDTNTITP QQLINIRPVI ASIKEFFGSS QLSQFMDQTN PLAEL THKR RLSALGPGGL TRERAGMEVR DVHYSHYGRM CPIETPEGPN IGLINSLSSY AKVNRFGFIE TPYRRVDPET GKVTGR IDY LTADEEDNYV VAQANARLDD EGAFIDDSIV ARFRGENTVV SRNRVDYMDV SPKQVVSAAT ACIPFLENDD SNRALMG AN MQRQAVPLMQ PEAPFVGTGM EYVSGKDSGA AVICKHPGIV ERVEAKNVWV RRYEEVDGQK VKGNLDKYSL LKFVRSNQ G TCYNQRPIVS VGDEVVKGEI LADGPSMELG ELALGRNVMV GFMTWDGYNY EDAIIMSERL VKDDVYTSIH IEEYESEAR DTKLGPEEIT RDIPNVGEDA LRNLDDRGII RIGAEVKDGD LLVGKVTPKG VTELTAEERL LHAIFGEKAR EVRDTSLRVP HGGGGIIHD VKVFNREDGD ELPPGVNQLV RVYIVQKRKI SEGDKMAGRH GNKGVISKIL PEEDMPYLPD GTPIDIMLNP L GVPSRMNI GQVLELHMGM AARYLGIHIA SPVFDGAREE DVWETLEEAG MSRDAKTVLY DGRTGEPFDN RVSVGIMYMI KL AHMVDDK LHARSTGPYS LVTQQPLGGK AQFGGQRFGE MEVWALEAYG AAYTLQEILT VKSDDVVGRV KTYEAIVKGD NVP EPGVPE SFKVLIKELQ SLGMDVKILS GDEEEIEMRD LEDEEDAKQA DGLALSGDEE PEETASADVE RDVVTKE

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
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)
Molecular weightTheoretical: 134.444953 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MLDVNNFEYM NIGLASPDKI RSWSFGEVKK PETINYRTLK PEKDGLFCER IFGPTKDWEC HCGKYKRVRY KGVVCDRCGV EVTRAKVRR ERMGHIELAA PVSHIWYFKG IPSRMGLVLD MSPRALEEVI YFASYVVTDP ANTPLEKKQL LSEKEYRAYL D KYGNKFQA ...String:
MLDVNNFEYM NIGLASPDKI RSWSFGEVKK PETINYRTLK PEKDGLFCER IFGPTKDWEC HCGKYKRVRY KGVVCDRCGV EVTRAKVRR ERMGHIELAA PVSHIWYFKG IPSRMGLVLD MSPRALEEVI YFASYVVTDP ANTPLEKKQL LSEKEYRAYL D KYGNKFQA SMGAEAIHKL LQDIDLVKEV DMLKEELKTS QGQRRTRAIK RLEVLEAFRN SGNKPSWMIL DVLPVIPPEL RP MVQLDGG RFATSDLNDL YRRVINRNNR LKRLLDLGAP SIIVQNEKRM LQEAVDALID NGRRGRPVTG PGNRPLKSLS HML KGKQGR FRQNLLGKRV DYSGRSVIVV GPHLKMYQCG LPKEMALELF KPFVMKELVE KGLAHNIKSA KRKIERVQPE VWDV LESVI KEHPVLLNRA PTLHRLGIQA FEPTLVEGRA IRLHPLVCTA YNADFDGDQM AVHVPLSAEA QAEARILMLA AQNIL NPKD GKPVVTPSQD MVLGNYYLTL ERAGAVGEGM VFKNTDEALL AYQNGYVHLH TRVAVAANSL KNVTFTEEQR SKLLIT TVG KLVFNEILPE SFPYMNEPTK SNIEEKTPDR FFLEKGADVK AVIAQQPINA PFKKGILGKI IAEIFKRFHI TETSKML DR MKNLGFKYST KAGITVGVSD IVVLDDKQEI LEEAQSKVDN VMKQFRRGLI TEEERYERVI SIWSAAKDVI QGKLMKSL D ELNPIYMMSD SGARGNASNF TQLAGMRGLM ANPAGRIIEL PIKSSFREGL TVLEYFISTH GARKGLADTA LKTADSGYL TRRLVDVAQD VIIRETDCGT DRGILAKPLK EGTETIERLE ERLIGRFARK QVKHPETGEV LVNENELIDE DKALEIVEAG IEEVWIRSA FTCNTPHGVC KRCYGRNLAT GSDVEVGEAV GIIAAQSIGE PGTQLTMRTF HTGGVAGDDI TQGLPRIQEL F EARNPKGQ ATITEIDGTV VEINEVRDKQ QEIVVQGAVE TRSYTAPYNS RLKVAEGDKI TRGQVLTEGS IDPKELLKVT DL TTVQEYL LHEVQKVYRM QGVEIGDKHV EVMVRQMLRK VRVIDAGDTD VLPGTLLDIH QFTEANKKVL LEGNRPATGR PVL LGITKA SLETDSFLSA ASFQETTRVL TDAAIKGKRD ELLGLKENVI IGKLVPAGTG MMKYRKVKPV SNVQPTDDMV PVE

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
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)
Molecular weightTheoretical: 7.766921 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MLDPSIDSLM NKLDSKYTLV TVSARRAREM QIKKDQMIEH TISHKYVGKA LEEIDAGLLS FEKEDRE

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: Bacillus (Bacillus rRNA group 1)
Molecular weightTheoretical: 43.007406 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MADKQTHETE LTFDQVKEQL TESGKKRGVL TYEEIAERMS SFEIESDQMD EYYEFLGEQG VELISENEET EDPNIQQLAK AEEEFDLND LSVPPGVKIN DPVRMYLKEI GRVNLLSAKE EIAYAQKIEE GDEESKRRLA EANLRLVVSI AKRYVGRGML F LDLIQEGN ...String:
MADKQTHETE LTFDQVKEQL TESGKKRGVL TYEEIAERMS SFEIESDQMD EYYEFLGEQG VELISENEET EDPNIQQLAK AEEEFDLND LSVPPGVKIN DPVRMYLKEI GRVNLLSAKE EIAYAQKIEE GDEESKRRLA EANLRLVVSI AKRYVGRGML F LDLIQEGN MGLMKAVEKF DYRKGYKFST YATWWIRQAI TRAIADQART IRIPVHMVET INKLIRVQRQ LLQDLGREPT PE EIAEDMD LTPEKVREIL KIAQEPVSLE TPIGEEDDSH LGDFIEDQEA TSPSDHAAYE LLKEQLEDVL DTLTDREENV LRL RFGLDD GRTRTLEEVG KVFGVTRERI RQIEAKALRK LRHPSRSKRL KDFLE

UniProtKB: RNA polymerase sigma factor SigA

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Macromolecule #6: Gene 33 protein

MacromoleculeName: Gene 33 protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage SPO1 (virus)
Molecular weightTheoretical: 11.92051 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MQKFLDELEK VRNHTEDYDV YNSEAERTFR GLKAKFQKLI GKRALYICKS TKESRVVTIE AAYDRYIVLS YKYYGMDYEG STKMSVTYQ ALLSGEDRLD VE

UniProtKB: Gene 33 protein

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Macromolecule #7: DNA-directed RNA polymerase subunit delta

MacromoleculeName: DNA-directed RNA polymerase subunit delta / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)
Molecular weightTheoretical: 20.417891 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MGIKQYSQEE LKEMALVEIA HELFEEHKKP VPFQELLNEI ASLLGVKKEE LGDRIAQFYT DLNIDGRFLA LSDQTWGLRS WYPYDQLDE ETQPTVKAKK KKAKKAVEED LDLDEFEEID EDDLDLDEVE EELDLEADDF DEEDLDEDDD DLEIEEDIID E DDEDYDDE EEEIK

UniProtKB: DNA-directed RNA polymerase subunit delta

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Macromolecule #8: DNA-directed RNA polymerase subunit epsilon

MacromoleculeName: DNA-directed RNA polymerase subunit epsilon / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)
Molecular weightTheoretical: 8.277386 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MIYKVFYQEK ADEVPVREKT DSLYIEGVSE RDIRTKLKEK KFNIEFITPV DGAFLEYEQQ SENFKVLEL

UniProtKB: DNA-directed RNA polymerase subunit epsilon

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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

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168575
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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