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- EMDB-27777: Streptomyces venezuelae RNAP transcription open promoter complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-27777
TitleStreptomyces venezuelae RNAP transcription open promoter complex with WhiA and WhiB transcription factors
Map dataStreptomyces venezuelae RNAP transcription open promoter complex with WhiA and WhiB transcription factors
Sample
  • Complex: Streptomyces venezuelae RNAP transcription open promoter complex with WhiA and WhiB transcription factors
    • Protein or peptide: x 8 types
    • DNA: x 2 types
  • Ligand: x 3 types
KeywordsRNA polymerase / Transcription factor / Iron cluster / TRANSCRIPTION-TRANSFERASE-DNA complex
Function / homology
Function and homology information


regulation of sporulation / dinitrosyl-iron complex binding / 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 / 4 iron, 4 sulfur cluster binding ...regulation of sporulation / dinitrosyl-iron complex binding / 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 / 4 iron, 4 sulfur cluster binding / protein dimerization activity / cell division / DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Sporulation regulator WhiA / Sporulation transcription regulator WhiA, N-terminal domain / Sporulation regulator WhiA, C-terminal / WhiA, LAGLIDADG-like domain / WhiA C-terminal HTH domain / WhiA N-terminal LAGLIDADG-like domain / WhiA LAGLIDADG-like domain / Transcription factor WhiB / WhiB-like iron-sulfur binding domain / Transcription factor WhiB ...Sporulation regulator WhiA / Sporulation transcription regulator WhiA, N-terminal domain / Sporulation regulator WhiA, C-terminal / WhiA, LAGLIDADG-like domain / WhiA C-terminal HTH domain / WhiA N-terminal LAGLIDADG-like domain / WhiA LAGLIDADG-like domain / Transcription factor WhiB / WhiB-like iron-sulfur binding domain / Transcription factor WhiB / 4Fe-4S WhiB-like (Wbl)-type iron-sulfur binding domain profile. / RNA polymerase-binding protein RbpA / RbpA superfamily / RNA polymerase-binding protein / Homing endonuclease / 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 / 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, 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 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
Transcriptional regulator WhiB / RNA polymerase sigma factor SigA / RNA polymerase-binding protein RbpA / DNA-directed RNA polymerase subunit omega / Probable cell division protein WhiA / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsLilic M / Campbell EA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structural basis of dual activation of cell division by the actinobacterial transcription factors WhiA and WhiB.
Authors: Mirjana Lilic / Neil A Holmes / Matthew J Bush / Alexandra K Marti / David A Widdick / Kim C Findlay / Young Joo Choi / Ruby Froom / Steven Koh / Mark J Buttner / Elizabeth A Campbell /
Abstract: Studies of transcriptional initiation in different bacterial clades reveal diverse molecular mechanisms regulating this first step in gene expression. The WhiA and WhiB factors are both required to ...Studies of transcriptional initiation in different bacterial clades reveal diverse molecular mechanisms regulating this first step in gene expression. The WhiA and WhiB factors are both required to express cell division genes in Actinobacteria and are essential in notable pathogens such as . The WhiA/B regulons and binding sites have been elucidated in (), where they coordinate to activate sporulation septation. However, how these factors cooperate at the molecular level is not understood. Here we present cryoelectron microscopy structures of transcriptional regulatory complexes comprising RNA polymerase (RNAP) σ-holoenzyme and WhiA and WhiB, in complex with the WhiA/B target promoter . These structures reveal that WhiB binds to domain 4 of σ (σ) of the σ-holoenzyme, bridging an interaction with WhiA while making non-specific contacts with the DNA upstream of the -35 core promoter element. The N-terminal homing endonuclease-like domain of WhiA interacts with WhiB, while the WhiA C-terminal domain (WhiA-CTD) makes base-specific contacts with the conserved WhiA GACAC motif. Notably, the structure of the WhiA-CTD and its interactions with the WhiA motif are strikingly similar to those observed between σ housekeeping σ-factors and the -35 promoter element, suggesting an evolutionary relationship. Structure-guided mutagenesis designed to disrupt these protein-DNA interactions reduces or abolishes developmental cell division in confirming their significance. Finally, we compare the architecture of the WhiA/B σ-holoenzyme promoter complex with the unrelated but model CAP Class I and Class II complexes, showing that WhiA/WhiB represent a new mechanism in bacterial transcriptional activation.
History
DepositionAug 3, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27777.png

Downloads & links

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Map

FileDownload / File: emd_27777.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStreptomyces venezuelae RNAP transcription open promoter complex with WhiA and WhiB transcription factors
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324.9 Å		1.08 Å/pix.
x 300 pix.
= 324.9 Å		1.08 Å/pix.
x 300 pix.
= 324.9 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 2.26
Minimum - Maximum-26.2057 - 42.181750000000001
Average (Standard dev.)0.0020328076 (±1.0102842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_27777_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
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Half map: Half Map 2

Fileemd_27777_half_map_2.map
AnnotationHalf Map 2
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Sample components

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Entire : Streptomyces venezuelae RNAP transcription open promoter complex ...

EntireName: Streptomyces venezuelae RNAP transcription open promoter complex with WhiA and WhiB transcription factors
Components
  • Complex: Streptomyces venezuelae RNAP transcription open promoter complex with WhiA and WhiB transcription factors
    • 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: RNA polymerase-binding protein RbpA
    • Protein or peptide: Transcriptional regulator WhiB
    • Protein or peptide: Probable cell division protein WhiA
    • DNA: DNA (78-MER)
    • DNA: DNA (71-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: Streptomyces venezuelae RNAP transcription open promoter complex ...

SupramoleculeName: Streptomyces venezuelae RNAP transcription open promoter complex with WhiA and WhiB transcription factors
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Streptomyces venezuelae (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: Streptomyces venezuelae (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Molecular weightTheoretical: 36.734641 KDa
SequenceString: MLIAQRPSLT EEVVDEFRSR FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTDLILNI KQLVVSSEH DEPVVMYLRK QGPGLVTAAD IAPPAGVEVH NPDLVLATLN GKGKLEMELT VERGRGYVSA VQNKQVGQEI G RIPVDSIY ...String:
MLIAQRPSLT EEVVDEFRSR FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTDLILNI KQLVVSSEH DEPVVMYLRK QGPGLVTAAD IAPPAGVEVH NPDLVLATLN GKGKLEMELT VERGRGYVSA VQNKQVGQEI G RIPVDSIY SPVLKVTYKV EATRVEQRTD FDKLIVDVET KQAMRPRDAM ASAGKTLVEL FGLARELNID AEGIDMGPSP TD AALAADL ALPIEELELT VRSYNCLKRE GIHSVGELVA RSEADLLDIR NFGAKSIDEV KAKLAGMGLA LKDSPPGFDP TAA ADAFGA DDDADAGFVE TEQY

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: Streptomyces venezuelae (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Molecular weightTheoretical: 130.458953 KDa
SequenceString: MQGTGTRVVS PSPRKDPLLA ASRNASTNTN NGASTAPLRI SFAKIKEPLE VPNLLALQTE SFDWLLGNAA WKARVEAALE SGQDVPTKS GLEEIFEEIS PIEDFSGSMS LTFRDHRFEP PKNSIDECKD RDFTYGAPLF VTAEFTNNET GEIKSQTVFM G DFPLMTNK ...String:
MQGTGTRVVS PSPRKDPLLA ASRNASTNTN NGASTAPLRI SFAKIKEPLE VPNLLALQTE SFDWLLGNAA WKARVEAALE SGQDVPTKS GLEEIFEEIS PIEDFSGSMS LTFRDHRFEP PKNSIDECKD RDFTYGAPLF VTAEFTNNET GEIKSQTVFM G DFPLMTNK GTFVINGTER VVVSQLVRSP GVYFDSSIDK TSDKDIFSAK IIPSRGAWLE MEIDKRDLVG VRIDRKRKQS VT VLLKALG WTTEQILQEF GEYESMRATL EKDHTQGQDD ALLDIYRKLR PGEPPTREAA QTLLENLYFN PKRYDLAKVG RYK VNKKLG ADEPLDAGVL TTDDVIATIK YLVKLHAGET ETIGENGNEI VVETDDIDHF GNRRLRNVGE LIQNQVRTGL ARME RVVRE RMTTQDVEAI TPQTLINIRP VVASIKEFFG TSQLSQFMDQ NNPLSGLTHK RRLSALGPGG LSRERAGFEV RDVHP SHYG RMCPIETPEG PNIGLIGSLA SYGRVNAFGF IETPYRKVVD GQVTDEVDYV TADEEDRFVI AQANAALDEE LRFSEN RVL VRKRGGEVDY VEPSDVDYMD VSPRQMVSVA TAMIPFLEHD DANRALMGAN MMRQAVPLIK SEAPLVGTGM EYRCATD AG DVLKAEKDGV VQELSADYIT VANDDGTYIT YRLHKFSRSN QGTSVNQKVV VDEGDRVIEG QVLADGPATE DGEMALGK N LLVAFMPWEG HNYEDAIILS QRLVQDDVLS SIHIEEHEVD ARDTKLGPEE ITRDIPNVSE EVLADLDERG IIRIGAEVV AGDILVGKVT PKGETELTPE ERLLRAIFGE KAREVRDTSL KVPHGEIGKI IGVRVFDREE GDELPPGVNQ LVRVYVAQKR KITDGDKLA GRHGNKGVIS KILPIEDMPF LEDGTPVDII LNPLGVPSRM NPGQVLEIHL GWLASRGWDV SGLADEWAQR L QAIGADKV APGTNVATPV FDGAREDELA GLLNHTIPNR DGERMVLPTG KARLFDGRSG EPFPDPISVG YMYILKLHHL VD DKLHARS TGPYSMITQQ PLGGKAQFGG QRFGEMEVWA LEAYGAAYAL QELLTIKSDD VTGRVKVYEA IVKGENIPEP GIP ESFKVL IKEMQSLCLN VEVLSSDGMS IEMRDTDEDV FRAAEELGID LSRREPSSVE EV

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: Streptomyces venezuelae (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Molecular weightTheoretical: 144.614781 KDa
SequenceString: DDVNFFDELR IGLATADDIR QWSHGEVKKP ETINYRTLKP EKDGLFCEKI FGPTRDWECY CGKYKRVRFK GIICERCGVE VTRAKVRRE RMGHIELAAP VTHIWYFKGV PSRLGYLLDL APKDLEKVIY FAAYMITYVD DERRTRDLPS LEAHVSVERQ Q IENRRDSD ...String:
DDVNFFDELR IGLATADDIR QWSHGEVKKP ETINYRTLKP EKDGLFCEKI FGPTRDWECY CGKYKRVRFK GIICERCGVE VTRAKVRRE RMGHIELAAP VTHIWYFKGV PSRLGYLLDL APKDLEKVIY FAAYMITYVD DERRTRDLPS LEAHVSVERQ Q IENRRDSD LEARAKKLEN DLGELEAEGA KADVRRKVRE GAEREMKQLR DRAQREIDRL DEVWSRFKNL KVQDLEGDEL LY RELRDRF GTYFDGSMGA AALQKRLESF DLEEEAERLR EIIRTGKGQK KTRALKRLKV VSAFLQTANS PKGMVLDCVP VIP PDLRPM VQLDGGRFAT SDLNDLYRRV INRNNRLKRL LDLGAPEIIV NNEKRMLQEA VDALFDNGRR GRPVTGPGNR PLKS LSDML KGKQGRFRQN LLGKRVDYSA RSVIVVGPQL KLHQCGLPKA MALELFKPFV MKRLVDLNHA QNIKSAKRMV ERGRT VVYD VLEEVIAEHP VLLNRAPTLH RLGIQAFEPQ LVEGKAIQIH PLVCTAFNAD FDGDQMAVHL PLSAEAQAEA RILMLS SNN ILKPADGRPV TMPTQDMVLG LFFLTTDGEL RDTKGEGRAF GSTAEAIMAF DAGELALQSQ IDIRFPVGTV APRGWVP PV TEEGEPEWQQ GDSFRLRTSL GRALFNELLP EDYPFVDYSV GKKQLSEIVN DLAERYPKVI VAATLDNLKA AGFYWATR S GVTVAISDVV VPEAKKAIVK GYEEQDEKVQ KQYERGLITK EERTQELIAI WTKATNEVAE AMNANFPKTN PIFMMVDSG ARGNMMQMRQ IAGMRGLVSN AKNETIPRPI KASFREGLTV LEYFISTHGA RKGLADTALR TADSGYLTRR LVDVSQDVII REEDCGTER GLKLRIAERG ADGVLRKTDD VETSVYARML AEDVVVDGKV IAPANVDLGD VLIDALVGAG VEEVKTRSVL T CESAVGTC AFCYGRSLAT GKLVDIGEAV GIIAAQSIGE PGTQLTMRTF HTGGVAGDDI TQGLPRVVEL FEARQPKGVA PI SEAAGRV RIEETEKTKK IVVTPDDGTD ETAFPISKRA RLLVGEGDHV EVGQKLTVGA TNPHDVLRIL GQRAVQVHLV AEV QKVYNS QGVSIHDKHI EIIIRQMLRR VTIIESGDAE LLPGELVERS KFETENRRVV TEGGHPASGR PQLMGITKAS LATE SWLSA ASFQETTRVL TDAAINAKSD SLIGLKENVI IGKLIPAGTG LSRYRNIRVE PTEEAKAAMY SAVGYDDIDY SPFGS GSGQ AVPLEDYDYG PYNQ

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: Streptomyces venezuelae (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Molecular weightTheoretical: 9.698903 KDa
SequenceString:
VSSSITAPEG IINPPIDELL EATDSKYSLV IYAAKRARQI NAYYSQLGEG LLEYVGPLVD THVHEKPLSI ALREINAGLL TSEAIEGPA Q

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: Streptomyces venezuelae (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Molecular weightTheoretical: 56.68018 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVSASTSRTL PPEIAESESV MALIERGKAD GQIAGDDVRR AFEADQIPPT QWKNVLRSLN QILEEEGVTL MVSAAESPKR ARKSVAAKS PAKRTATKTV TARTTVTKTT VTAAPASAAE DADPADEAGS AAKKTAAKKT VAKKTVAKKT VAKKTAAKKT T SKKDADEL ...String:
MVSASTSRTL PPEIAESESV MALIERGKAD GQIAGDDVRR AFEADQIPPT QWKNVLRSLN QILEEEGVTL MVSAAESPKR ARKSVAAKS PAKRTATKTV TARTTVTKTT VTAAPASAAE DADPADEAGS AAKKTAAKKT VAKKTVAKKT VAKKTAAKKT T SKKDADEL VEGEELLEDV APGKGEEEET EGESKGFVLS DEDEDDAPAQ QVAVAGATAD PVKDYLKQIG KVPLLNAEQE VE LAKRIEA GLFAEDKLAN SDKLAPKLKR ELEIIAEDGR RAKNHLLEAN LRLVVSLAKR YTGRGMLFLD LIQEGNLGLI RAV EKFDYT KGYKFSTYAT WWIRQAITRA MADQARTIRI PVHMVEVINK LARVQRQMLQ DLGREPTPEE LAKELDMTPE KVIE VQKYG REPISLHTPL GEDGDSEFGD LIEDSEAVVP ADAVSFTLLQ EQLHSVLDTL SEREAGVVSM RFGLTDGQPK TLDEI GKVY GVTRERIRQI ESKTMSKLRH PSRSQVLRDY LD

UniProtKB: RNA polymerase sigma factor SigA

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Macromolecule #6: RNA polymerase-binding protein RbpA

MacromoleculeName: RNA polymerase-binding protein RbpA / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces venezuelae (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Molecular weightTheoretical: 14.116112 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSERALRGTR LVVTSYETDR GIDLAPRQAV EYACEKGHRF EMPFSVEAEI PPEWECKVCG IQALLVDGDG PEEKKGKPAR THWDMLMER RTREELEEVL AERLAVLRSG AMNIAVHPRD SRKSA

UniProtKB: RNA polymerase-binding protein RbpA

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Macromolecule #7: Transcriptional regulator WhiB

MacromoleculeName: Transcriptional regulator WhiB / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces venezuelae (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Molecular weightTheoretical: 10.069341 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTELFQELLV EDADEELGWQ ERALCAQTDP ESFFPEKGGS TREAKKVCLA CEVRSECLEY ALQNDERFGI WGGLSERERR RLKKKAV

UniProtKB: Transcriptional regulator WhiB

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Macromolecule #8: Probable cell division protein WhiA

MacromoleculeName: Probable cell division protein WhiA / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces venezuelae (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Molecular weightTheoretical: 37.956402 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH HHHHSSGLEV LFQGPHMTAA VKDEISRLPV TRTCCRKAEV SSILRFAGGL HLVSGRIVIE AELDTAMAAR RLKRDILEI FGHSSELIVM APGGLRRGSR FVVRVVAGGD QLARQTGLVD GRGRPIRGLP PQVVSGATCD AEAAWRGAFL A HGSLTEPG ...String:
MGSSHHHHHH HHHHSSGLEV LFQGPHMTAA VKDEISRLPV TRTCCRKAEV SSILRFAGGL HLVSGRIVIE AELDTAMAAR RLKRDILEI FGHSSELIVM APGGLRRGSR FVVRVVAGGD QLARQTGLVD GRGRPIRGLP PQVVSGATCD AEAAWRGAFL A HGSLTEPG RSSSLEVTCP GPEAALALVG AARRLSIAAK AREVRGVDRV VVRDGDAIGA LLTRLGAHES VLAWEERRMR RE VRATANR LANFDDANLR RSARAAVAAG ARVQRALEIL GEEVPEHLAA AGRLRMEHKQ ASLEELGALA DPPLTKDAVA GRI RRLLAM ADKRAQDLGI PGTESNLTEE LDDSLVG

UniProtKB: Probable cell division protein WhiA

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Macromolecule #9: DNA (78-MER)

MacromoleculeName: DNA (78-MER) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Streptomyces venezuelae (bacteria)
Molecular weightTheoretical: 30.769604 KDa
SequenceString: (DG)(DT)(DG)(DA)(DT)(DA)(DT)(DC)(DA)(DG) (DC)(DC)(DA)(DG)(DA)(DT)(DC)(DG)(DT)(DG) (DC)(DG)(DA)(DC)(DA)(DC)(DA)(DC)(DC) (DG)(DG)(DG)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DG) (DC)(DC)(DG)(DA)(DT)(DG) ...String:
(DG)(DT)(DG)(DA)(DT)(DA)(DT)(DC)(DA)(DG) (DC)(DC)(DA)(DG)(DA)(DT)(DC)(DG)(DT)(DG) (DC)(DG)(DA)(DC)(DA)(DC)(DA)(DC)(DC) (DG)(DG)(DG)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DG) (DC)(DC)(DG)(DA)(DT)(DG)(DC)(DC) (DG)(DT)(DC)(DC)(DC)(DG)(DC)(DG)(DA)(DA) (DC)(DC) (DC)(DC)(DT)(DC)(DT)(DA)(DC) (DC)(DG)(DT)(DG)(DT)(DG)(DA)(DG)(DG)(DC) (DG)(DT)(DG) (DA)(DG)(DC)(DA)(DG)(DC) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DA) (DT)(DC)(DT)(DA)

GENBANK: GENBANK: CP018074.1

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Macromolecule #10: DNA (71-MER)

MacromoleculeName: DNA (71-MER) / type: dna / ID: 10 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Streptomyces venezuelae (bacteria)
Molecular weightTheoretical: 30.942676 KDa
SequenceString: (DT)(DA)(DG)(DA)(DT)(DG)(DA)(DG)(DG)(DC) (DC)(DG)(DC)(DT)(DG)(DC)(DT)(DG)(DC)(DT) (DC)(DA)(DC)(DG)(DC)(DC)(DT)(DC)(DA) (DC)(DA)(DC)(DG)(DG)(DT)(DA)(DG)(DA)(DG) (DG) (DG)(DG)(DT)(DT)(DC)(DG) ...String:
(DT)(DA)(DG)(DA)(DT)(DG)(DA)(DG)(DG)(DC) (DC)(DG)(DC)(DT)(DG)(DC)(DT)(DG)(DC)(DT) (DC)(DA)(DC)(DG)(DC)(DC)(DT)(DC)(DA) (DC)(DA)(DC)(DG)(DG)(DT)(DA)(DG)(DA)(DG) (DG) (DG)(DG)(DT)(DT)(DC)(DG)(DC)(DG) (DG)(DG)(DA)(DC)(DG)(DG)(DC)(DA)(DT)(DC) (DG)(DG) (DC)(DC)(DA)(DA)(DT)(DT)(DG) (DG)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DT)(DG) (DT)(DC)(DG) (DC)(DA)(DC)(DG)(DA)(DT) (DC)(DT)(DG)(DG)(DC)(DT)(DG)(DA)(DT)(DA) (DT)(DC)(DA)(DC)

GENBANK: GENBANK: CP018074.1

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #13: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 13 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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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: 51.44 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7kif

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 184251
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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