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- EMDB-21852: F. tularensis RNAPs70-(MglA-SspA)-ppGpp-PigR-iglA DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-21852
TitleF. tularensis RNAPs70-(MglA-SspA)-ppGpp-PigR-iglA DNA complex
Map dataF. tularensis RNAPs70-(MglA-SspA)-ppGpp-PigR-iglA DNA unsharpened map
Sample
  • Complex: Francisella RNAPs70-(MglA-SspA)-ppGpp-PigR-iglA DNA complex
    • Protein or peptide: x 9 types
    • DNA: x 4 types
  • Ligand: x 3 types
KeywordsRNA polymerase complex / TRANSCRIPTION
Function / homology
Function and homology information


sigma factor activity / glutathione metabolic process / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / transferase activity / protein dimerization activity / DNA-templated transcription ...sigma factor activity / glutathione metabolic process / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / transferase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
: / Macrophage Locus Protein A, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Glutathione S-transferase, C-terminal domain ...: / Macrophage Locus Protein A, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Glutathione S-transferase, C-terminal domain / 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 / Glutathione transferase family / 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 / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / 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 / 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 / Thioredoxin-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
RNA polymerase sigma factor RpoD / GST N-terminal domain-containing protein / Glutathione S-transferase / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit alpha 2 / DNA-directed RNA polymerase subunit alpha 1
Similarity search - Component
Biological speciesFrancisella tularensis subsp. holarctica LVS (bacteria) / Francisella tularensis subsp. holarctica (strain LVS) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.43 Å
AuthorsTravis BA / Brennan RG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: Mol Cell / Year: 2021
Title: Structural Basis for Virulence Activation of Francisella tularensis.
Authors: Brady A Travis / Kathryn M Ramsey / Samantha M Prezioso / Thomas Tallo / Jamie M Wandzilak / Allen Hsu / Mario Borgnia / Alberto Bartesaghi / Simon L Dove / Richard G Brennan / Maria A Schumacher /
Abstract: The bacterium Francisella tularensis (Ft) is one of the most infectious agents known. Ft virulence is controlled by a unique combination of transcription regulators: the MglA-SspA heterodimer, PigR, ...The bacterium Francisella tularensis (Ft) is one of the most infectious agents known. Ft virulence is controlled by a unique combination of transcription regulators: the MglA-SspA heterodimer, PigR, and the stress signal, ppGpp. MglA-SspA assembles with the σ-associated RNAP holoenzyme (RNAPσ), forming a virulence-specialized polymerase. These factors activate Francisella pathogenicity island (FPI) gene expression, which is required for virulence, but the mechanism is unknown. Here we report FtRNAPσ-promoter-DNA, FtRNAPσ-(MglA-SspA)-promoter DNA, and FtRNAPσ-(MglA-SspA)-ppGpp-PigR-promoter DNA cryo-EM structures. Structural and genetic analyses show MglA-SspA facilitates σ binding to DNA to regulate virulence and virulence-enhancing genes. Our Escherichia coli RNAPσhomodimeric EcSspA structure suggests this is a general SspA-transcription regulation mechanism. Strikingly, our FtRNAPσ-(MglA-SspA)-ppGpp-PigR-DNA structure reveals ppGpp binding to MglA-SspA tethers PigR to promoters. PigR in turn recruits FtRNAP αCTDs to DNA UP elements. Thus, these studies unveil a unique mechanism for Ft pathogenesis involving a virulence-specialized RNAP that employs two (MglA-SspA)-based strategies to activate virulence genes.
History
DepositionApr 21, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wmt
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wmt
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21852.png

Downloads & links

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Map

FileDownload / File: emd_21852.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationF. tularensis RNAPs70-(MglA-SspA)-ppGpp-PigR-iglA DNA unsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 352 pix.
= 376.64 Å		1.07 Å/pix.
x 352 pix.
= 376.64 Å		1.07 Å/pix.
x 352 pix.
= 376.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004 / Movie #1: 0.004
Minimum - Maximum-0.0070203277 - 0.026299901
Average (Standard dev.)0.000005024636 (±0.0011479633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 376.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z376.640376.640376.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.0070.0260.000

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Supplemental data

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Sample components

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Entire : Francisella RNAPs70-(MglA-SspA)-ppGpp-PigR-iglA DNA complex

EntireName: Francisella RNAPs70-(MglA-SspA)-ppGpp-PigR-iglA DNA complex
Components
  • Complex: Francisella RNAPs70-(MglA-SspA)-ppGpp-PigR-iglA DNA complex
    • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha 1
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha 2
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • DNA: DNA NT-strand
    • DNA: DNA T-strand
    • DNA: DNA T-strand downstream
    • Protein or peptide: aCTDs
    • Protein or peptide: Macrophage growth locus, subunit A
    • Protein or peptide: Glutathione S-transferase
    • DNA: DNA NT-strand downstream
    • Protein or peptide: RNA polymerase sigma factor RpoD
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: GUANOSINE-5',3'-TETRAPHOSPHATE

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Supramolecule #1: Francisella RNAPs70-(MglA-SspA)-ppGpp-PigR-iglA DNA complex

SupramoleculeName: Francisella RNAPs70-(MglA-SspA)-ppGpp-PigR-iglA DNA complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Francisella tularensis subsp. holarctica LVS (bacteria)

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Macromolecule #1: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Francisella tularensis subsp. holarctica (strain LVS) (bacteria)
Strain: LVS
Molecular weightTheoretical: 8.184333 KDa
SequenceString:
MARVTVEDCL DKVETRFDLV VLASMRANKI LKNGYSESME NEKKEKATVV ALREIAESEI TSEQILRNEI EG

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #2: DNA-directed RNA polymerase subunit alpha 1

MacromoleculeName: DNA-directed RNA polymerase subunit alpha 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Francisella tularensis subsp. holarctica (strain LVS) (bacteria)
Strain: LVS
Molecular weightTheoretical: 35.393387 KDa
SequenceString: MSNNNSKLEF VPNIQLKEDL GAFSYKVQLS PVEKGMAHIL GNSIRRVLLS SLSGASIIKV NIANVLHEYS TLEDVKEDVV EIVSNLKKV AIKLDTGIDR LDLELSVNKS GVVSAGDFKT TQGVEIINKD QPIATLTNQR AFSLTATVSV GRNVGILSAI P TELERVGD ...String:
MSNNNSKLEF VPNIQLKEDL GAFSYKVQLS PVEKGMAHIL GNSIRRVLLS SLSGASIIKV NIANVLHEYS TLEDVKEDVV EIVSNLKKV AIKLDTGIDR LDLELSVNKS GVVSAGDFKT TQGVEIINKD QPIATLTNQR AFSLTATVSV GRNVGILSAI P TELERVGD IAVDADFNPI KRVAFEVFDN GDSETLEVFV KTNGTIEPLA AVTKALEYFC EQISVFVSLR VPSNGKTGDV LI DSNIDPI LLKPIDDLEL TVRSSNCLRA ENIKYLGDLV QYSESQLMKI PNLGKKSLNE IKQILIDNNL SLGVQIDNFR ELV EGK

UniProtKB: DNA-directed RNA polymerase subunit alpha 1

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Macromolecule #3: DNA-directed RNA polymerase subunit alpha 2

MacromoleculeName: DNA-directed RNA polymerase subunit alpha 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Francisella tularensis subsp. holarctica (strain LVS) (bacteria)
Strain: LVS
Molecular weightTheoretical: 35.113031 KDa
SequenceString: MALENLLHPT NIKIDEYAKN ATKFSFEALE RGVGYTLGFA LKQTMLYSIA GACVTSIKIN DGKVTSLEDV IPCDETVADI ILNVKSLSV TLAEDVETGT ITFELSGSEE EIFSEEAKLS EGLAITEEVF ICSYNGGKKL KIEAKVEKGV GFRPAQDNFK D GEFLLDAT ...String:
MALENLLHPT NIKIDEYAKN ATKFSFEALE RGVGYTLGFA LKQTMLYSIA GACVTSIKIN DGKVTSLEDV IPCDETVADI ILNVKSLSV TLAEDVETGT ITFELSGSEE EIFSEEAKLS EGLAITEEVF ICSYNGGKKL KIEAKVEKGV GFRPAQDNFK D GEFLLDAT FSPVVFCDFE IKDARVGRRT DLDKLELNIK TNGNVNCEEA LRLAATKIQN QLRNIVDIEE INKGIFVEDP KD INPILLK HVEELNLTAR SSNCLKAVNI RLIGELVQKT ENELLKAPNF GKKSLTEIKD KLSELGLSLG TLIENWPQDL

UniProtKB: DNA-directed RNA polymerase subunit alpha 2

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Macromolecule #4: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Francisella tularensis subsp. holarctica (strain LVS) (bacteria)
Strain: LVS
Molecular weightTheoretical: 151.536141 KDa
SequenceString: MSYSYAEKKR IRKEFGVLPH ILDVPYLLSI QTESYKKFLT VDAAKGRLHS GLEIVLKQSF PVESKNGQYE LHYVDYQIGE PTFDETECQ VRGATYDAPL NVKLRLVVYN KDALPNEKIV EDIREEYVYM GDIPLMTTNG TFIINGTERV VVSQLHRSPG A FFSKDDSE ...String:
MSYSYAEKKR IRKEFGVLPH ILDVPYLLSI QTESYKKFLT VDAAKGRLHS GLEIVLKQSF PVESKNGQYE LHYVDYQIGE PTFDETECQ VRGATYDAPL NVKLRLVVYN KDALPNEKIV EDIREEYVYM GDIPLMTTNG TFIINGTERV VVSQLHRSPG A FFSKDDSE EGAFSARIIP YRGSWLDFEF DSKGIIWARI DRKRKFCATV ILKALGYTQE QILENFSESK TITFNSKGFA LR LDNLSNM KGELLKFDIV DAQDNVIVKK NKKLTSRDVK KIKDAGVDSV AIDFDLVSTL RVAKDIVNEA TGEVIAYAND DVT ESLLKS CVEVGMLELE VIDFITTERG RYISDTLKYD LTRNTDEALV EIYKVLRPGD PPAAASVKAL FEGLFFIESR YSLS DIGRM KLNARLGSDK VSKDIYTLEN SDIVGVIEEL INIRDGKGKV DDIDHLGNRR VRSVGEMVEN QFRIGLYRVE KGIRE SMSL VHKDKLMPKD IVNSKPITAA IKEFFTSGAL SQFMDQDNPL SEVTHKRRIS ALGPGGLSRD RAGFEVRDVH ATHYGR LCP IETPEGPNIG LINSLASYAR VNDYGFLEAP YRKVVDGKVT DEIEYLSAID EDNYVIAQAS TKLDENNHFV EDIIQCR SG GEAIFTESSR VQYMDVSAKQ MVSAAAALIP FLEHDDANRV LMGANMQRQA VPTLKSEKPL VGTGMEKIVA RDSGNCII A RNVGEVAEVD SNRIVIKVDT EKSQTSNLVD IYSLTKFKRS NKNTCINQRP IVNVGDKVEA GDILADGFAT DFGELSLGH NLMVAFMPWN GYNFEDSILL SERIVKDDKY TSIHIEEFTC VARDTKLGPE EITADIPNVS ESSLAKLDES GIVHIGANVE AGDILVAKI TPKAEQQLTP EERLLRAIFN EKASNVVDSS LRMPSGTSGT VINVQVFEND KGGKSKRALK IEKELIDKAR K DFDEEFAV IESVVKSSIE QEVVGAKIQK AKGLKKGAIL TKEFLATLPL SKWLEISFED EKLEEKVQNA REYYEEAKIA ID AKFEAKK KSITQSNELS PGVLKTVKVF VAIKKRIQPG DKMAGRHGNK GVVSRVLPVE DMPYMEDGTP VDVCLNPLGI PSR MNIGQI LEAHLGLASY GLGKKIEKTL EKTRKAAELR KTLEEVYNSV GDKKVNLEAL NDEEILTLCD NLKGGVPIAT PVFD GAKEE DIKSLLKIGG FATNGQMKLF DGRTGKPFDR HVTVGYMYML KLDHLVDDKM HARSTGSYSL VTQQPLGGKA QFGGQ RFGE MEVWALQAYG AAYTLREMLT VKSDDIAGRS KMYKNIVDGK LTMNVDVPES FNVLRNEVRA LGIDMDFDYS SEEE

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #5: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Francisella tularensis subsp. holarctica LVS (bacteria)
Strain: LVS
Molecular weightTheoretical: 178.4455 KDa
SequenceString: MNNGILHQNY NSKKFDIIKI SLASPEVIRS WSHGEVKKPE TINYRTFKPE RDGLFCAKIF GPIKDYECLC GKYKRLKHRG VVCERCGVE VEQAKVRRER MGHIDLVCPV VHIWYLKSLP SRIGLFLDMP LKNVEKVLYF ESYIVTDPGM TPLEKKQLLT D EEYAEALE ...String:
MNNGILHQNY NSKKFDIIKI SLASPEVIRS WSHGEVKKPE TINYRTFKPE RDGLFCAKIF GPIKDYECLC GKYKRLKHRG VVCERCGVE VEQAKVRRER MGHIDLVCPV VHIWYLKSLP SRIGLFLDMP LKNVEKVLYF ESYIVTDPGM TPLEKKQLLT D EEYAEALE NYGYEFEASM GAEAIRDLLA DTDIESEIEL LQAECEESKS TAKKEKAIKR LRLLETFQAS GNKPEWMVMT VL PVLPPDL RPLVPIEGGR FATSDLNDLY RRVINRNNRL KKLLDLNAPD IIVRNEKRML QEAVDALLDN GRRGRAVTGS NKR PLKSLA DMIKGKQGRF RQNLLGKRVD YSGRSVITVG PSLRLHECGL PKKMALELFK PFVYSKLRLG GHATTIKQAK RMVE LEEAV VWDILETVIN EHPVLLNRAP TLHRLGIQAF EPRLIEGKAI QLHPLVCAAF NADFDGDQMA VHVPLTVESQ LEARV LMMS TNNILSPASG QPIITPTQDI VLGLYYITRE KEGARGEGKL FSSYEDVSRA YNSGTIDIHA KIKLRIDRQV FDTKGN TYN EKGVVNTTVG RALLLNILPE GLSFSLLNKV LVKKEISKII NQAFRVLGGK ATVVLADKLM YAGFKYSTLS GVSVGVD DM TIPDNKEAKI EEAEKEIKQI TEQYQSSLIT ENERYNNIIN IWSKTSDEVG ASMMDAISKD TVSINGEKKE IESFNSVY M MAKSGARGSY NQMRQLAGMR GLMAKPDGTM IETAITANFR EGLSVLQYFT STHGARKGLA DTALKTANAG YLTRRLVDV AQDLVVIEED CGTDDGLMFS AIVEDGEVKV PLVERALGRT LAADVVTEKG VVLLEAGTLL DENLVELLDD NGIDMIKVRS PITCKTRRG LCAKCYGRDL ARERQVNVGE SVGVIAAQSI GEPGTQLTMR TFHTGGAASL GITVSDIKVK TAGKIKFKNI R TVTNKEGQ EIVISRAGEI IVSDTMGRVR EQHKIPMGAV VPLASGKAVE IGDVIATWDP HAQPLITDVA GKVVLEDVID GI TSKHTYD DLTGQQTIEI TSISQRTTSK NLKPVVKIVD EKGAELKSIP LAVGAVLNVA DDSILEVGDI VAKIPLEGSK NKD ITGGLP RVAELFEARR PKDAAILSPC DGMVRLGNRD TKEKQRIEII DKNGHIVEEI LLPKSRHLVV FDGEQVSRGD VLAD GPTDP HDLLKYKGLE EFADYILIEA QSVYRMQGVV INDKHIETIV RQMLRKAVIL DEGDSKFVKD ESIELVRILE ENDKL RKQG KKEVEYELVL MGITRSSLST ESFLSAASFQ ETTRVLTEAS INSQIDNLRG LKENVLIGRL IPAGTGLAVR KESAKI EKM REELGVEDNM VFTDLSSFNP EEISFDSIQS QKEDKDINED IEESLRNALE SLDFAAASME KRRWKKNFIA VSAANRF KK ISSSGALDYD IPTTASENLY FQGELKTAAL AQHDEAVDNK FNKEQQNAFY EILHLPNLNE EQRNAFIQSL KDDPSQSA N LLAEAKKLND AQAPKVDNKF NKEQQNAFYE ILHLPNLNEE QRNAFIQSLK DDPSQSANLL AEAKKLNGAQ APKVDANSA GKST

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Macromolecule #9: aCTDs

MacromoleculeName: aCTDs / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Francisella tularensis subsp. holarctica LVS (bacteria)
Molecular weightTheoretical: 6.230672 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #10: Macrophage growth locus, subunit A

MacromoleculeName: Macrophage growth locus, subunit A / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Francisella tularensis subsp. holarctica LVS (bacteria)
Molecular weightTheoretical: 23.650656 KDa
SequenceString: MLLYTKKDDI YSDIVRMILL IKGANAKIVD VSKEENSKHL EELNIITPNG NIPTLSTDDF AVYRLSVIIE AIEDLYPFPP MFPVFPKQR ANARILLEYV NKTFLQNIIK LQSPDLDEKQ ANEIKMLMQR DIISTYKKIV SEREVNAESN PDAQNINVLT L IITFVFYY ...String:
MLLYTKKDDI YSDIVRMILL IKGANAKIVD VSKEENSKHL EELNIITPNG NIPTLSTDDF AVYRLSVIIE AIEDLYPFPP MFPVFPKQR ANARILLEYV NKTFLQNIIK LQSPDLDEKQ ANEIKMLMQR DIISTYKKIV SEREVNAESN PDAQNINVLT L IITFVFYY FIKLKISIPT KDKNIIKEIK ELLSEPNFIK TIKAKGA

UniProtKB: GST N-terminal domain-containing protein

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Macromolecule #11: Glutathione S-transferase

MacromoleculeName: Glutathione S-transferase / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Francisella tularensis subsp. holarctica LVS (bacteria)
Molecular weightTheoretical: 24.098213 KDa
SequenceString: MMKVTLYTTK YCPYSLRARI ALAEKKMSTD IVEAGDLEPA MIKKITPNGV FPVLMEKDYS INNRKALLIY IDERFPAPSL LPNVVNERI KIRLSLDKID NEWYPVLDQI RKHRSDQKML ESMFKDLKES LLAMEKAFTG SEFFISSGFT LADCYIAALI I CLEAEGFI ...String:
MMKVTLYTTK YCPYSLRARI ALAEKKMSTD IVEAGDLEPA MIKKITPNGV FPVLMEKDYS INNRKALLIY IDERFPAPSL LPNVVNERI KIRLSLDKID NEWYPVLDQI RKHRSDQKML ESMFKDLKES LLAMEKAFTG SEFFISSGFT LADCYIAALI I CLEAEGFI IDDEYGAIYE YKKRLFARDS VKKANIKGGA GESLLKTLRT HR

UniProtKB: Glutathione S-transferase

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Macromolecule #13: RNA polymerase sigma factor RpoD

MacromoleculeName: RNA polymerase sigma factor RpoD / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Francisella tularensis subsp. holarctica LVS (bacteria)
Molecular weightTheoretical: 67.748469 KDa
SequenceString: MTKEDLLSDL KDLMIDGRER GYLTRADILD ALPGDVSEDP KIYEEIEAIL IDAGIDVYDR TPQIEEDDER KVSEANLDDL KGKTSDPIR MYMREMGIVD LLDKKGETDI AIRIEEGTTE VFSTILSYPI VIKTYIERFR ELEEKAIDYM NSQDIENEPV A RYIRFNEV ...String:
MTKEDLLSDL KDLMIDGRER GYLTRADILD ALPGDVSEDP KIYEEIEAIL IDAGIDVYDR TPQIEEDDER KVSEANLDDL KGKTSDPIR MYMREMGIVD LLDKKGETDI AIRIEEGTTE VFSTILSYPI VIKTYIERFR ELEEKAIDYM NSQDIENEPV A RYIRFNEV MAGFSDEQVT EEKVAEDDHE EKIDTQRAYE FFTNLEKMFE EYQDKPNKKL YTKIVKEFDN LRLSTSHLQK LV DYIRLPY ARVKEFERKI LRLCVERSKT PRQEFIKVYK VGSLEWLEPL TKKYKFTENT IREIKNLTKQ INQFQILMMM DIE ELKQVN LEISRSEAKI TQAKKEMIEA NLRLVVSEAK KYTNRGLHFL DIIQEGNIGL MKAVDKFDYR KGFKFSTYAT WWIR QAITR SIADQARTIR VPVHMIETIN KVNRIKRQIL QEKGREATEE EIIEHTPNMS KEKLKKILNI SHTPISMESP IGDDE DSTV GDFIEDKNNY SPIEAANLEN LREAIKELIE TGLTEREAKV LMMRFGIGMN TDHTLEEVGK QFNVTRERIR QIEAKA LRK LKHPSRSAFL KTFL

UniProtKB: RNA polymerase sigma factor RpoD

+
Macromolecule #6: DNA NT-strand

MacromoleculeName: DNA NT-strand / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Francisella tularensis subsp. holarctica LVS (bacteria)
Molecular weightTheoretical: 16.074336 KDa
SequenceString: (DA)(DT)(DT)(DT)(DA)(DG)(DC)(DT)(DG)(DT) (DA)(DT)(DA)(DA)(DA)(DC)(DA)(DT)(DT)(DG) (DT)(DG)(DT)(DT)(DA)(DT)(DT)(DG)(DG) (DC)(DG)(DT)(DT)(DA)(DT)(DT)(DA)(DA)(DG) (DG) (DT)(DA)(DA)(DC)(DT)(DT) ...String:
(DA)(DT)(DT)(DT)(DA)(DG)(DC)(DT)(DG)(DT) (DA)(DT)(DA)(DA)(DA)(DC)(DA)(DT)(DT)(DG) (DT)(DG)(DT)(DT)(DA)(DT)(DT)(DG)(DG) (DC)(DG)(DT)(DT)(DA)(DT)(DT)(DA)(DA)(DG) (DG) (DT)(DA)(DA)(DC)(DT)(DT)(DG)(DC) (DT)(DT)(DA)(DT)

GENBANK: GENBANK: AM233362.1

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Macromolecule #7: DNA T-strand

MacromoleculeName: DNA T-strand / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Francisella tularensis subsp. holarctica LVS (bacteria)
Molecular weightTheoretical: 12.83333 KDa
SequenceString:
(DT)(DA)(DC)(DC)(DT)(DT)(DA)(DA)(DT)(DA) (DA)(DC)(DG)(DC)(DC)(DA)(DA)(DT)(DA)(DA) (DC)(DA)(DC)(DA)(DA)(DT)(DG)(DT)(DT) (DT)(DA)(DT)(DA)(DC)(DA)(DG)(DC)(DT)(DA) (DA) (DA)(DT)

+
Macromolecule #8: DNA T-strand downstream

MacromoleculeName: DNA T-strand downstream / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Francisella tularensis subsp. holarctica LVS (bacteria)
Molecular weightTheoretical: 3.359199 KDa
SequenceString:
(DG)(DC)(DC)(DG)(DC)(DG)(DT)(DC)(DA)(DG) (DA)

+
Macromolecule #12: DNA NT-strand downstream

MacromoleculeName: DNA NT-strand downstream / type: dna / ID: 12 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Francisella tularensis subsp. holarctica LVS (bacteria)
Molecular weightTheoretical: 3.350185 KDa
SequenceString:
(DT)(DC)(DT)(DG)(DA)(DC)(DG)(DC)(DG)(DG) (DC)

+
Macromolecule #14: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 14 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #15: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 15 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #16: GUANOSINE-5',3'-TETRAPHOSPHATE

MacromoleculeName: GUANOSINE-5',3'-TETRAPHOSPHATE / type: ligand / ID: 16 / Number of copies: 2 / Formula: G4P
Molecular weightTheoretical: 603.16 Da
Chemical component information

ChemComp-G4P:
GUANOSINE-5',3'-TETRAPHOSPHATE

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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

Concentration0.4 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 116936
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6wmt:
F. tularensis RNAPs70-(MglA-SspA)-ppGpp-PigR-iglA DNA complex

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