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- EMDB-47312: Consensus map for the composite map of RpaA bound to PkaiBC DNA a... -

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Basic information

Entry
Database: EMDB / ID: EMD-47312
TitleConsensus map for the composite map 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
KeywordsSigA / RNAP / TAC / RpaA / Response regulator / transcriptional regulator / DNA BINDING PROTEIN
Biological speciesSynechococcus elongatus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 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: Nat Struct Mol Biol / Year: 2026
Title: Mechanism and reconstitution of circadian transcription in cyanobacteria.
Authors: Mingxu Fang / Yajie Gu / Miron Leanca / Mariusz Matyszewski / Andy LiWang / Yulia Yuzenkova / Kevin D Corbett / Susan S Golden /
Abstract: Circadian biological clocks evolved across kingdoms of life as an adaptation to predictable cycles of sunrise and sunset. In the cyanobacterium Synechococcus elongatus, a protein-based clock ...Circadian biological clocks evolved across kingdoms of life as an adaptation to predictable cycles of sunrise and sunset. In the cyanobacterium Synechococcus elongatus, a protein-based clock precisely controls when different genes are turned on and off during the 24-h day but the phasing mechanism remains unclear. Here we show the molecular basis of this regulation and reconstitute clock-controlled transcription in vitro using purified components. Biochemical and structural analyses revealed that the clock-regulated transcription factor RpaA can function as either an activator or a repressor of cyanobacterial RNA polymerase, depending on its binding position relative to core promoter elements. Leveraging the repressor mechanism, we developed a heterologous in vitro system driven by bacteriophage T7 RNA polymerase that sustains circadian transcription for multiple days. These findings explain how a single clock output generates opposite phases of gene expression and define the minimal components for circadian clock function, enabling synthetic or biotechnological applications.
History
DepositionOct 14, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47312.png

Downloads & links

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Map

FileDownload / File: emd_47312.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 600 pix.
= 561. Å		0.94 Å/pix.
x 600 pix.
= 561. Å		0.94 Å/pix.
x 600 pix.
= 561. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.3842116 - 0.8022001
Average (Standard dev.)-0.000083138126 (±0.0106708575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 561.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47312_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47312_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

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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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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 correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 83966
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8syi


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

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