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- EMDB-47222: Cryo-EM structure of RpaA bound to PkaiBC DNA and the CTD of the ... -

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Basic information

Entry
Database: EMDB / ID: EMD-47222
TitleCryo-EM structure of RpaA bound to PkaiBC DNA and the CTD of the alpha subunit of RNAP from the cyanobacterium Synechococcus elongatus
Map data
Sample
  • Complex: CryoEM structure of Syn7942 RNAP-SigA holoenzyme
    • DNA: Non-template DNA
    • DNA: Template DNA
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: RNA polymerase sigma factor SigA1
    • Protein or peptide: DNA-binding dual master transcriptional regulator RpaA
Keywordsalpha subunit of RNAP / PkaiBC DNA / RpaA / transcription factor / 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 / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / transcription cis-regulatory region binding ...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 / 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 / DNA binding / cytoplasm / cytosol
Similarity search - Function
RNA polymerase sigma factor, RpoD-like, cyanobacteria / 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 factor, RpoD-like, cyanobacteria / 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 / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
RNA polymerase sigma factor SigA1 / DNA-directed RNA polymerase subunit alpha / 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: 3.74 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_47222.png

Downloads & links

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Map

FileDownload / File: emd_47222.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.)
1.4 Å/pix.
x 400 pix.
= 561. Å		1.4 Å/pix.
x 400 pix.
= 561. Å		1.4 Å/pix.
x 400 pix.
= 561. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4025 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.59008753 - 1.0937015
Average (Standard dev.)-0.00014668076 (±0.014773131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 561.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47222_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47222_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CryoEM structure of Syn7942 RNAP-SigA holoenzyme

EntireName: CryoEM structure of Syn7942 RNAP-SigA holoenzyme
Components
  • Complex: CryoEM structure of Syn7942 RNAP-SigA holoenzyme
    • DNA: Non-template DNA
    • DNA: Template DNA
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: RNA polymerase sigma factor SigA1
    • Protein or peptide: DNA-binding dual master transcriptional regulator RpaA

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Supramolecule #1: CryoEM structure of Syn7942 RNAP-SigA holoenzyme

SupramoleculeName: CryoEM structure of Syn7942 RNAP-SigA holoenzyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3, #5, #4
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: 1 / 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-binding dual master transcriptional regulator RpaA

MacromoleculeName: DNA-binding dual master transcriptional regulator RpaA
type: protein_or_peptide / ID: 4 / 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 #5: RNA polymerase sigma factor SigA1

MacromoleculeName: RNA polymerase sigma factor SigA1 / type: protein_or_peptide / ID: 5 / 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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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 Active 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: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81192
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9dvt:
Cryo-EM structure of RpaA bound to PkaiBC DNA and the CTD of the alpha subunit of RNAP from the cyanobacterium Synechococcus elongatus

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