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- EMDB-47223: CryoEM structure of RpaA bound to PkaiBC DNA and Syn7942 RNAP-Sig... -

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Basic information

Entry
Database: EMDB / ID: EMD-47223
TitleCryoEM structure of RpaA bound to PkaiBC DNA and Syn7942 RNAP-SigA holoenzyme
Map data
Sample
  • Complex: RpaA dimer bound to PkaiBC DNA and Syn7942 RNAP-SigA holoenzyme
    • DNA: x 2 types
    • Protein or peptide: x 7 types
  • Ligand: x 2 types
KeywordsSigA / RNAP / TAC / RpaA / Response regulator / transcriptional regulator / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


circadian regulation of translation / phosphorelay response regulator activity / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / protein-DNA complex / circadian rhythm / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity ...circadian regulation of translation / phosphorelay response regulator activity / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / protein-DNA complex / circadian rhythm / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / transcription cis-regulatory region binding / protein dimerization activity / cell division / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
RNA polymerase sigma factor, RpoD-like, cyanobacteria / DNA-directed RNA polymerase, subunit gamma / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector ...RNA polymerase sigma factor, RpoD-like, cyanobacteria / DNA-directed RNA polymerase, subunit gamma / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / 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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / DNA-directed RNA polymerase, omega subunit / 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, 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
RNA polymerase sigma factor SigA1 / DNA-directed RNA polymerase subunit gamma / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-binding dual master transcriptional regulator RpaA
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria) / synthetic construct (others) / Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsFang M / Gu Y / Matyszewski M / Leanca M / LiWang A / Yuzenkova Y / Corbett KD / Golden SE
Funding support United States, United Kingdom, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM144121 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118290 United States
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W017385/1 United Kingdom
CitationJournal: To Be Published
Title: Reconstitution of Circadian Transcription in vitro through RpaA Regulation
Authors: Fang M / Gu Y / Leanca M / Matyszewski M / LiWang A / Yuzenkova Y / Corbett KD / Golden SE
History
DepositionOct 8, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47223.png

Downloads & links

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Map

FileDownload / File: emd_47223.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 400 pix.
= 478.72 Å		1.2 Å/pix.
x 400 pix.
= 478.72 Å		1.2 Å/pix.
x 400 pix.
= 478.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1968 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.11101024 - 1.0172105
Average (Standard dev.)0.005596063 (±0.018862247)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 478.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : RpaA dimer bound to PkaiBC DNA and Syn7942 RNAP-SigA holoenzyme

EntireName: RpaA dimer bound to PkaiBC DNA and Syn7942 RNAP-SigA holoenzyme
Components
  • Complex: RpaA dimer bound to PkaiBC DNA and Syn7942 RNAP-SigA holoenzyme
    • DNA: Non-template DNA
    • DNA: Template DNA
    • 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 gamma
    • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • Protein or peptide: RNA polymerase sigma factor SigA1
    • Protein or peptide: DNA-binding dual master transcriptional regulator RpaA
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: RpaA dimer bound to PkaiBC DNA and Syn7942 RNAP-SigA holoenzyme

SupramoleculeName: RpaA dimer bound to PkaiBC DNA and Syn7942 RNAP-SigA holoenzyme
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Synechococcus elongatus (bacteria)

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Macromolecule #1: Non-template DNA

MacromoleculeName: Non-template DNA / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 32.396689 KDa
SequenceString: (DC)(DT)(DG)(DA)(DA)(DA)(DA)(DC)(DC)(DT) (DG)(DA)(DA)(DA)(DA)(DG)(DG)(DT)(DA)(DA) (DA)(DG)(DG)(DA)(DG)(DG)(DT)(DC)(DT) (DT)(DA)(DA)(DG)(DC)(DT)(DC)(DG)(DG)(DC) (DT) (DC)(DA)(DA)(DT)(DT)(DT) ...String:
(DC)(DT)(DG)(DA)(DA)(DA)(DA)(DC)(DC)(DT) (DG)(DA)(DA)(DA)(DA)(DG)(DG)(DT)(DA)(DA) (DA)(DG)(DG)(DA)(DG)(DG)(DT)(DC)(DT) (DT)(DA)(DA)(DG)(DC)(DT)(DC)(DG)(DG)(DC) (DT) (DC)(DA)(DA)(DT)(DT)(DT)(DC)(DT) (DC)(DT)(DC)(DT)(DT)(DT)(DA)(DT)(DC)(DC) (DT)(DG) (DT)(DT)(DA)(DG)(DA)(DT)(DG) (DG)(DT)(DT)(DT)(DG)(DA)(DT)(DT)(DG)(DC) (DT)(DG)(DT) (DT)(DG)(DC)(DT)(DA)(DC) (DC)(DC)(DC)(DG)(DT)(DT)(DG)(DA)(DT)(DC) (DT)(DG)(DC)(DG) (DT)(DA)(DT)(DG)(DA)

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Macromolecule #2: Template DNA

MacromoleculeName: Template DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 32.384795 KDa
SequenceString: (DT)(DC)(DA)(DT)(DA)(DC)(DG)(DC)(DA)(DG) (DA)(DT)(DC)(DA)(DA)(DC)(DG)(DG)(DG)(DG) (DT)(DA)(DG)(DC)(DA)(DA)(DC)(DA)(DG) (DC)(DA)(DA)(DT)(DC)(DA)(DA)(DA)(DC)(DC) (DA) (DT)(DC)(DT)(DA)(DA)(DC) ...String:
(DT)(DC)(DA)(DT)(DA)(DC)(DG)(DC)(DA)(DG) (DA)(DT)(DC)(DA)(DA)(DC)(DG)(DG)(DG)(DG) (DT)(DA)(DG)(DC)(DA)(DA)(DC)(DA)(DG) (DC)(DA)(DA)(DT)(DC)(DA)(DA)(DA)(DC)(DC) (DA) (DT)(DC)(DT)(DA)(DA)(DC)(DA)(DG) (DG)(DA)(DT)(DA)(DA)(DA)(DG)(DA)(DG)(DA) (DG)(DA) (DA)(DA)(DT)(DT)(DG)(DA)(DG) (DC)(DC)(DG)(DA)(DG)(DC)(DT)(DT)(DA)(DA) (DG)(DA)(DC) (DC)(DT)(DC)(DC)(DT)(DT) (DT)(DA)(DC)(DC)(DT)(DT)(DT)(DT)(DC)(DA) (DG)(DG)(DT)(DT) (DT)(DT)(DC)(DA)(DG)

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Macromolecule #3: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 33.814891 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTFQVECVES RTEADQGQYG RFSIEPLARG QGTTVGNALR RVLLSNLEGT AVTAVRIGGV NHEFATIPGV REDVLDILLN VRELVVHAH SPQPQIGRLR VVGPATVTAA DVDFGPEVEV INPNHYIASL SEGATLEMEL KVEWGTGYRA IDRSHDETTA L DFLQLDAV ...String:
MTFQVECVES RTEADQGQYG RFSIEPLARG QGTTVGNALR RVLLSNLEGT AVTAVRIGGV NHEFATIPGV REDVLDILLN VRELVVHAH SPQPQIGRLR VVGPATVTAA DVDFGPEVEV INPNHYIASL SEGATLEMEL KVEWGTGYRA IDRSHDETTA L DFLQLDAV FMPVRRVNYS VEDARVGEST AIDRLVLEVW TNGSLSPQEA LSQAASCLVA LFEPLKNVSV GSTHTADPEP TP ESQTPIE DLQLSVRAYN CLKRAQVNSV ADLLSYTYED LLEIKNFGQK SAEEVVEALE RIGIKLQESK VS

UniProtKB: DNA-directed RNA polymerase subunit alpha

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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: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 123.428547 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAEQTQLAPA AFHLPDLVAI QRNSFRWFLE EGLIEELESF SPITDYTGKL ELHFLGKQYK LKRPKYDVDE AKRRDGTYSV QMYVPTRLI NKETGEIKEQ EVFIGDLPLM TDRGTFIING AERVIVNQIV RSPGVYYKSE RDKNGRLTHN ASLIPNRGAW L KFETDKNG ...String:
MAEQTQLAPA AFHLPDLVAI QRNSFRWFLE EGLIEELESF SPITDYTGKL ELHFLGKQYK LKRPKYDVDE AKRRDGTYSV QMYVPTRLI NKETGEIKEQ EVFIGDLPLM TDRGTFIING AERVIVNQIV RSPGVYYKSE RDKNGRLTHN ASLIPNRGAW L KFETDKNG LVWVRIDKTR KLSAQVLLKA LGLSDNEIYD KLRHPEYYQK TIDKEGQFSE DEALMELYRK LRPGEPPTVS GG QQLLESR FFDPKRYDLG RVGRYKLNKK LGLNVADTVR TLTSEDILAA IDYLINLELD LGGCEVDDID HLGNRRVRSV GEL LQNQVR VGLNRLERII RERMTVSDSD SLSPASLVNP KPLVAAIKEF FGSSQLSQFM DQTNPLAELT HKRRLSALGP GGLT RERAG FAVRDIHPSH YGRICPIETP EGPNAGLIGS LATHARVNDY GFIETPFWRV EEGRVRKDLA PVYMTADQED DLRVA PGDV ATDDAGYILG TTIPVRYRQD FTTTTPERVD YVALSPVQII SVATSLIPFL EHDDANRALM GSNMQRQAVP LLRPER PLV GTGLEPQAAR DSGMVITSPV DGTISYVDAT HIEVTADTGE KYGYALQKYQ RSNQDTCLNQ RPIVFEGDRV QRGQVIA DG SATEKGELAL GQNILVAYMP WEGYNYEDAI LISERLVYDD VYTSIHIEKF EIEARQTKLG PEEITREIPN VGEDALRQ L DENGIIRVGA WVESGDILVG KVTPKGESDQ PPEEKLLRAI FGEKARDVRD NSLRVPNGEK GRVVDVRLFT REQGDELPP GANMVVRVYV AQKRKIQVGD KMAGRHGNKG IISRILPCED MPYLPDGTPL DIVLNPLGVP SRMNVGQVFE CMLGWAGQLL DARFKVTPF DEMYGAEASR LTVNAKLSEA REQTGQPWVF SDDEPGKIQV YDGRTGEPFD RPVTVGRAYM LKLVHLVDDK I HARSTGPY SLVTQQPLGG KAQQGGQRFG EMEVWALEAY GAAYILQELL TVKSDDMQGR NEALNAIVKG KAIPRPGTPE SF KVLMREL QSLCLDIAVY KASTEDYEED KEVDLMADVN QRRTPSRPTY ESMSVGDIDD DDD

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #5: DNA-directed RNA polymerase subunit gamma

MacromoleculeName: DNA-directed RNA polymerase subunit gamma / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 71.054367 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAKQEQRFDY VKIALASPER IRQWGERTLP NGQVVGEVTK PETINYRTLK PEMDGLFCEK IFGPAKDWEC HCGKYKRVRH RGIVCERCG VEVTESRVRR HRMGFIKLAA PVAHVWYLKG IPSYIAILLD MPLRDVEQIV YFNSYVVLNP GNHSELQYKQ L LNEDQWME ...String:
MAKQEQRFDY VKIALASPER IRQWGERTLP NGQVVGEVTK PETINYRTLK PEMDGLFCEK IFGPAKDWEC HCGKYKRVRH RGIVCERCG VEVTESRVRR HRMGFIKLAA PVAHVWYLKG IPSYIAILLD MPLRDVEQIV YFNSYVVLNP GNHSELQYKQ L LNEDQWME IEDQIYAEES DLEGIEVGIG AEALQQLLQD LNLNEESEKL RQEIAESKGQ KRAKLIKRLR VIDNFIGTES RP EWMVLNV IPVIPPDLRP MVQLDGGRFA TSDLNDLYRR VINRNNRLAR LQEILAPEII VRNEKRMLQE AVDALIDNGR RGR TVVGAN NRPLKSLSDI IEGKQGRFRQ NLLGKRVDYS GRSVIVVGPN LKIHQCGLPR EMAIELFQPF VIHRLIKNHS INNI KQAKK LIQKNDPLIW DVLEEVIEGH PVMLNRAPTL HRLGIQAFEP ILVEGRAIQL HPLVCPAFNA DFDGDQMAVH VPLSI EAQA EARMLMLASG NILSPATGQP IVTPSQDMVL GCYYLTAENP GAQKGAGRYF ANLEDAIRAF EQGSVDLHAW VWVRFD GEV ESEGESDEPE SVVAADDGTV TKTYRFRRIR ETEDGQRLSQ YVKTTPGRIL FNNTVQTALI H

UniProtKB: DNA-directed RNA polymerase subunit gamma

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Macromolecule #6: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 8.787966 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MLQRFDLDSQ DLLFKAESLI VNSTNRYHVT LQIARRAKQA RYEEMENLSE ETGIKPVLRA ILEMSDELNQ PEIIGG

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #7: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 144.006031 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAEAKSAPIF RNRVIDKKQL KKLIGWTFAH YGTAKTAVVA DDLKALGFRY ATRAGVSISI DDLKVPGSKA ELLESAEKRI QETEDRYTR GEITEVERFQ KVIDTWANTN DELTDRVVKN FRESDPLNSV YMMAFSGARG NISQVRQLVG MRGLMANPQG E IIDLPIKT ...String:
MAEAKSAPIF RNRVIDKKQL KKLIGWTFAH YGTAKTAVVA DDLKALGFRY ATRAGVSISI DDLKVPGSKA ELLESAEKRI QETEDRYTR GEITEVERFQ KVIDTWANTN DELTDRVVKN FRESDPLNSV YMMAFSGARG NISQVRQLVG MRGLMANPQG E IIDLPIKT NFREGLTVTE YIISSYGARK GLVDTALRTA DSGYLTRRLV DVSQDVIIHE VDCGTSRGLF VEAMTDGDRI LI PISQRLL GRVTAEAVLD PSTDEVLAEA GQDINEDLAN RIEKAGIKKV KVRSPLTCEA ARSVCQKCYG WSLAHAQMVD MGE AVGIIA AQSIGEPGTQ LTMRTFHTGG VFTGETARLL RAPVAGTIKL GKKARTRPYR TRHGEEALLA EANFDLVLEG KGRK ETFAI LQGSTIFVQD GDKVAAEAIL AEVPVSGRTK RTVEKATKDV ATDLAGEIRF QDIVPEEKTD RQGNTTRIAQ RGGLL WVLA GDVYNLLPGA EPTVKNGDRV EVGDVLAETK LTTERGGTVR MGEDNGSSTH REVEIITASV VLDTATVKAE ASQGRE HYV IETKGGQRFN LLAAPGTKVT TGHVVAELID SRYRTQTGGL LKYSGVEISK KGRAKAKQGY EVTKGGTLLW IPEETHE VN KDISLLNVED GQLVEAGTEV VKDIFCQTTG IVSVTQNNDI LREIVIKPGD VHVLDDPDTA AKYDEGRLVN AGEEVFPG L TAEQLVWAEA VDGTDGPLLL LRPVQELVIP DEPPVPSQDS SQESSSRSIR LRAVQRLQFQ DGERIKSVEG VDLLRTQLV LESEEGSSQL SADIELLPDS KDPETLRLQL VIIEPVVIRR DVASDTTHGS THTELRVKDG QKVKPGAVIA CTQIQCKEAG VVRGIQEGS EAVRRLLVER ERDCVTLDLD VTAATQLQPG SLIVAGTQLV DGIIAPESGE VRAIAPGQLQ LRIARPYRVS Q GAVLHVED KGLVQRGDNL VLLVFERAKT GDIIQGLPRI EELLEARKPK EACILARRPG VAHINYSDDD AIDIQVIEAD GT QADYPVG PGQPLIISDG ETVDAGQALT DGPANPHDLL EIYYDYFREQ LGEDYEAALE SLRRVQALLV NEVQSVYQSQ GID ISDKHI EVIVRQMTSK VRIDDGGDTI MLPGELHELR EVYNSNNTMA LTGMAPAQFT PVLLGITKAS LNTNSFISAA SFQE TTRVL TEAAIEGKSD WLRGLKENVI IGRLIPAGTG FKAYEESLLT DVDGGYEDRV YDDDLADVVI DDRAARSYTL NEGRD FSRS MTFAEGESMI LDDGEELIDD SSASLRNLVD VDED

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #8: RNA polymerase sigma factor SigA1

MacromoleculeName: RNA polymerase sigma factor SigA1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Strain: ATCC 33912 / PCC 7942 / FACHB-805
Molecular weightTheoretical: 45.776234 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTQLISIDKE QEEAGMTQAT ELLDPALKPA ETKAKRSSRK KATTAVVEPA TTIAPTADVD AIDDEDSVGE DEDAAAKAKA KVRKTYTED SIRLYLQEIG RIRLLRADEE IELARQIADL LALERIRDEL LEQLDRLPSD AEWAAAVDSP LDEFRRRLFR G RRAKDKMV ...String:
MTQLISIDKE QEEAGMTQAT ELLDPALKPA ETKAKRSSRK KATTAVVEPA TTIAPTADVD AIDDEDSVGE DEDAAAKAKA KVRKTYTED SIRLYLQEIG RIRLLRADEE IELARQIADL LALERIRDEL LEQLDRLPSD AEWAAAVDSP LDEFRRRLFR G RRAKDKMV QSNLRLVVSI AKKYMNRGLS FQDLIQEGSL GLIRAAEKFD HEKGYKFSTY ATWWIRQAIT RAIADQSRTI RL PVHLYET ISRIKKTTKL LSQEMGRKPT EEEIATRMEM TIEKLRFIAK SAQLPISLET PIGKEEDSRL GDFIEADGET PED EVAKNL LREDLEGVLS TLSPRERDVL RLRYGLDDGR MKTLEEIGQL FNVTRERIRQ IEAKALRKLR HPNRNSILKE YIR

UniProtKB: RNA polymerase sigma factor SigA1

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Macromolecule #9: DNA-binding dual master transcriptional regulator RpaA

MacromoleculeName: DNA-binding dual master transcriptional regulator RpaA
type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Strain: ATCC 33912 / PCC 7942 / FACHB-805
Molecular weightTheoretical: 28.582727 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKPRILVIDD DSAILELVAV NLEMSGYDVR KAEDGIKGQA LAVQLVPDLI ML(PHD)LMLPRVD GFTVCQRLRR DERTAE IPV LMLTALGQTQ DKVEGFNAGA DDYLTKPFEV EEMLARVRAL LQRTDRIPHA ARHSEILSYG PLTLIPERFE AIWFNRT VK LTHLEFELLH ...String:
MKPRILVIDD DSAILELVAV NLEMSGYDVR KAEDGIKGQA LAVQLVPDLI ML(PHD)LMLPRVD GFTVCQRLRR DERTAE IPV LMLTALGQTQ DKVEGFNAGA DDYLTKPFEV EEMLARVRAL LQRTDRIPHA ARHSEILSYG PLTLIPERFE AIWFNRT VK LTHLEFELLH CLLQRHGQTV APSEILKEVW GYDPDDDIET IRVHIRHLRT KLEPDPRHPR YIKTVYGAGY CLELPAET E LHQHADQFPS AS

UniProtKB: DNA-binding dual master transcriptional regulator RpaA

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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
Details: 20 mM Tris pH 8.0, 50 mM NaCl, 5 mM MgCl2 and 5% glycerol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 221552
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

8syi


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9dvu:
CryoEM structure of RpaA bound to PkaiBC DNA and Syn7942 RNAP-SigA holoenzyme

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