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

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Basic information

Entry
Database: PDB / ID: 9dvu
TitleCryoEM structure of RpaA bound to PkaiBC DNA and Syn7942 RNAP-SigA holoenzyme
Components
  • (DNA-directed RNA polymerase subunit ...) x 5
  • DNA-binding dual master transcriptional regulator RpaA
  • Non-template DNA
  • RNA polymerase sigma factor SigA1
  • Template DNA
KeywordsDNA BINDING PROTEIN/DNA / SigA / 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 / cytosol / cytoplasm
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, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / 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 Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / 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
DNA / DNA (> 10) / DNA (> 100) / 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)
Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsFang, M. / Gu, Y. / Matyszewski, M. / Leanca, M. / LiWang, A. / Yuzenkova, Y. / Corbett, K.D. / Golden, S.E.
Funding support United States, United Kingdom, 3items
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, K.D. / Golden, S.E.
History
DepositionOct 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Non-template DNA
2: Template DNA
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit gamma
E: DNA-directed RNA polymerase subunit omega
F: DNA-directed RNA polymerase subunit beta'
G: RNA polymerase sigma factor SigA1
R: DNA-binding dual master transcriptional regulator RpaA
S: DNA-binding dual master transcriptional regulator RpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)582,78514
Polymers582,63011
Non-polymers1553
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 2 types, 2 molecules 12

#1: DNA chain Non-template DNA


Mass: 32396.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain Template DNA


Mass: 32384.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA-directed RNA polymerase subunit ... , 5 types, 6 molecules ABCDEF

#3: Protein DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 33814.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Gene: rpoA, Synpcc7942_2209 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q31L30, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 123428.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Gene: rpoB, Synpcc7942_1522 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q31N17, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase subunit gamma / RNAP subunit gamma / RNA polymerase subunit gamma / Transcriptase subunit gamma


Mass: 71054.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Gene: rpoC1, Synpcc7942_1523 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42079, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 8787.966 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Gene: rpoZ, Synpcc7942_1710 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q31MH9, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 144006.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Gene: rpoC2, Synpcc7942_1524 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q31N15, DNA-directed RNA polymerase

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Protein , 2 types, 3 molecules GRS

#8: Protein RNA polymerase sigma factor SigA1


Mass: 45776.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Strain: ATCC 33912 / PCC 7942 / FACHB-805 / Gene: sigA1, rpoD1, Synpcc7942_0649 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38023
#9: Protein DNA-binding dual master transcriptional regulator RpaA / Regulator of phycobilisome-associated protein A / RpaA


Mass: 28582.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Strain: ATCC 33912 / PCC 7942 / FACHB-805 / Gene: rpaA, Synpcc7942_0095 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q31S42

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Non-polymers , 2 types, 3 molecules

#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RpaA dimer bound to PkaiBC DNA and Syn7942 RNAP-SigA holoenzyme
Type: COMPLEX / Entity ID: #1-#9 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Synechococcus elongatus (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET28b
Buffer solutionpH: 8
Details: 20 mM Tris pH 8.0, 50 mM NaCl, 5 mM MgCl2 and 5% glycerol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 221552 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8SYI

8syi


Accession code: 8SYI / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 116.33 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005936054
ELECTRON MICROSCOPYf_angle_d0.752349311
ELECTRON MICROSCOPYf_chiral_restr0.04795628
ELECTRON MICROSCOPYf_plane_restr0.01256069
ELECTRON MICROSCOPYf_dihedral_angle_d17.634313989

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