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- EMDB-53913: Consensus reconstruction of the PrPfr hybrid state of the Pseudom... -

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Basic information

Entry
Database: EMDB / ID: EMD-53913
TitleConsensus reconstruction of the PrPfr hybrid state of the Pseudomonas aeruginosa bacteriophytochrome / PaBphP
Map data
Sample
  • Complex: Photochromic heterodimerimer of the bacterial phytochrome PaBphP
KeywordsPhytochrome / Bacteriophytochrome / Photoreceptor / Histidine kinase / CYTOSOLIC PROTEIN
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBodizs S / Westenhoff S
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: J Am Chem Soc / Year: 2025
Title: Chemical Mechanism of Allosteric and Asymmetric Dark Reversion in a Bacterial Phytochrome Uncovered by Cryo-EM.
Authors: Szabolcs Bódizs / Anna-Lena M Fischer / Miklós Cervenak / Sayan Prodhan / Michal Maj / Sebastian Westenhoff /
Abstract: Phytochromes are light-sensitive proteins that are found in plants, fungi, and bacteria. They exist in two functional states, Pr and Pfr, distinguished by / isomers of their bilin chromophore. The ...Phytochromes are light-sensitive proteins that are found in plants, fungi, and bacteria. They exist in two functional states, Pr and Pfr, distinguished by / isomers of their bilin chromophore. The chromophore can photoswitch between these states but also thermally converts in darkness. Despite the importance of the latter reaction, it is unknown how it is controlled by the phytochrome's structure. Here, we present single-particle cryo-EM measurements on the bacteriophytochrome (PaBphP) carried out at multiple time points during dark reversion from Pr to Pfr. These experiments resolved the structure of a PrPfr hybrid state as a transient intermediate. Surprisingly, we find that only protomer B converts back to Pfr in the hybrid, while protomer A remains in Pr. We identify structural asymmetries in the precursor Pr state, which extend from the homodimer interface to a conserved histidine (H277). The hydrogen-bonding network around the chromophore is modulated, explaining how a phytochrome exerts control over the isomerization reaction. These findings establish that dark reversion is governed by conformational selection between two substates, whereby one is "dark-reversion ready" and the other blocks the reaction. Moreover, we explain how the equilibrium of the states is allosterically controlled across the dimer. Together, these findings provide a structural framework for tuning phytochrome signaling lifetimes in optogenetic applications.
History
DepositionMay 27, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53913.png

Downloads & links

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Map

FileDownload / File: emd_53913.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.39411822 - 0.76458454
Average (Standard dev.)-0.000014285335 (±0.008791232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53913_msk_1.map
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Half map: #2

Fileemd_53913_half_map_1.map
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Half map: #1

Fileemd_53913_half_map_2.map
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Sample components

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Entire : Photochromic heterodimerimer of the bacterial phytochrome PaBphP

EntireName: Photochromic heterodimerimer of the bacterial phytochrome PaBphP
Components
  • Complex: Photochromic heterodimerimer of the bacterial phytochrome PaBphP

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Supramolecule #1: Photochromic heterodimerimer of the bacterial phytochrome PaBphP

SupramoleculeName: Photochromic heterodimerimer of the bacterial phytochrome PaBphP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 160 KDa

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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

Concentration1.5 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
80.0 mMC4H11NO3Tris
10.0 mMMgCl2Magnesium chloride
150.0 mMCH3CO2KPotassium acetate
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 40.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 14573 / Average exposure time: 1.8 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6) / Type: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 488190
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.6)
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.6)

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