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- EMDB-73612: Pr-Pfr heterodimer state of Stigmatella aurantiaca bacteriophytoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-73612
TitlePr-Pfr heterodimer state of Stigmatella aurantiaca bacteriophytochrome 2
Map data
Sample
  • Organelle or cellular component: Stigmatella aurantiaca bacteriophytochrome
    • Protein or peptide: Bacteriophytochrome
  • Ligand: BILIVERDINE IX ALPHA
KeywordsSignal Transduction / Photoactivation / SIGNALING PROTEIN
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / phosphorelay sensor kinase activity / histidine kinase / photoreceptor activity / protein kinase activator activity / regulation of DNA-templated transcription
Similarity search - Function
Phytochrome / : / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...Phytochrome / : / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Biological speciesStigmatella aurantiaca (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.01 Å
AuthorsKarki P / Stojkovic EA / Schmidt M
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Simons Foundation United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Commun Chem / Year: 2026
Title: A bacteriophytochrome Pr/Pfr heterodimer studied through single-particle time-resolved cryo-electron microscopy.
Authors: Prabin Karki / William C Budell / Rohit Kannachel / David Menendez / Carolina Hernandez / Joshua H Mendez / Shemiran Kanou / Manjeet Singh / Chavdar Slavov / Peter Schwander / Tek Narsingh ...Authors: Prabin Karki / William C Budell / Rohit Kannachel / David Menendez / Carolina Hernandez / Joshua H Mendez / Shemiran Kanou / Manjeet Singh / Chavdar Slavov / Peter Schwander / Tek Narsingh Malla / Emina A Stojković / Marius Schmidt /
Abstract: Phytochromes are dimeric photoreceptors found in bacteria, fungi, and plants that reversibly interconvert between a red-absorbing Pr state and a far-red-absorbing Pfr state. In bacteria, phytochromes ...Phytochromes are dimeric photoreceptors found in bacteria, fungi, and plants that reversibly interconvert between a red-absorbing Pr state and a far-red-absorbing Pfr state. In bacteria, phytochromes (BphPs) regulate diverse responses through a two-component signaling pathway comprising a C-terminal histidine kinase (HK) and a response regulator. A previous cryo-EM study of the wild-type BphP from Stigmatella aurantiaca (SaBphP2) revealed a stable Pr/Pfr heterodimer in which the two protomers adopt distinct Pr and Pfr conformations. Here, using the Spotiton technique, we captured the same heterodimer by illuminating SaBphP2 particles on the cryo-EM grid and vitrifying them 10 ms later. Comparison with the Pr/Pr homodimer reveals a 180° rotation of the HK domain, driven by an unwinding of the coiled-coil helices that connect the photosensory core to the enzymatic domain. The large-scale reorientations provide mechanistic insight into light-triggered signal transduction mediated by bacterial phytochromes.
History
DepositionOct 27, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73612.png

Downloads & links

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Map

FileDownload / File: emd_73612.map.gz / Format: CCP4 / Size: 163.6 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.)
0.86 Å/pix.
x 350 pix.
= 299.6 Å		0.86 Å/pix.
x 350 pix.
= 299.6 Å		0.86 Å/pix.
x 350 pix.
= 299.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0226
Minimum - Maximum-0.062426485 - 0.22527672
Average (Standard dev.)0.00017713258 (±0.007330804)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73612_msk_1.map
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Half map: #2

Fileemd_73612_half_map_1.map
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Half map: #1

Fileemd_73612_half_map_2.map
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Sample components

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Entire : Stigmatella aurantiaca bacteriophytochrome

EntireName: Stigmatella aurantiaca bacteriophytochrome
Components
  • Organelle or cellular component: Stigmatella aurantiaca bacteriophytochrome
    • Protein or peptide: Bacteriophytochrome
  • Ligand: BILIVERDINE IX ALPHA

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Supramolecule #1: Stigmatella aurantiaca bacteriophytochrome

SupramoleculeName: Stigmatella aurantiaca bacteriophytochrome / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Stigmatella aurantiaca (bacteria)
Molecular weightTheoretical: 81 KDa

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Macromolecule #1: Bacteriophytochrome

MacromoleculeName: Bacteriophytochrome / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: histidine kinase
Source (natural)Organism: Stigmatella aurantiaca (bacteria)
Molecular weightTheoretical: 80.249688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ELSQCDREPI HLLGGIQAYG VLLAFRGPDR RLEVVSANTQ ALLGRPPEAL LGKTAAQVLP AELWAQWELL SARGALRVAL PSGPYRALL HESDGLTVLE LEPAELQPDM EETALELVRR LVSPLAGAKG TRELLQTAAN TVRALTGFDR VMVYRFDADW H GEVLAESK ...String:
ELSQCDREPI HLLGGIQAYG VLLAFRGPDR RLEVVSANTQ ALLGRPPEAL LGKTAAQVLP AELWAQWELL SARGALRVAL PSGPYRALL HESDGLTVLE LEPAELQPDM EETALELVRR LVSPLAGAKG TRELLQTAAN TVRALTGFDR VMVYRFDADW H GEVLAESK REGMDGFLGM HFPATDIPVQ ARALYTRNPL RLIANARARP VPLVPSVVPE LGRPLDLSGS ALRSVSPIHL EY LRNMGVE ASFSLSLLKD GALWGLIACH HLAPLHLSYE RRRACEVLTQ LLALQLSSEE RAAEAAEDSH RAALLGPLAT SLG AGGTLE EALAKDGARV LELTGATGAA LLLGGEPLLV GRTPSMDEVE ALAAWLAPQP FQTSFHTERL GSLYPPLAAR ADVA AGLLA VRLAPASSRL ALWFRPEAVR TISWAGNPRK PAEPEPGHAR LHPRGSFQAW EETVRETSPA WKRADLAAAE GFRSA LIGV VLRQAAELER LSEALSRSNA ELDAFGHTVA HDLKEPLRGI QQYAGFVMED YHGALGPEGR GHMESLMWLA QRSGDM LDG LFEYSRAGRV DLAWGEVNMQ EVVDEVLATL STRFQAEKLT VRMPRRLPTV RCDGIRIAQV WANLLVNAAK YQEGPER WV EAGFHGPGEP RPGAAGRYAS AYVFYVKDPG IGIAPPFHEA IFEMFRRLHS AKAYGGGTGV GLAIARRLVQ LHGGALWV D SAPKQGATFY FTLGRGPG

UniProtKB: histidine kinase

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Macromolecule #2: BILIVERDINE IX ALPHA

MacromoleculeName: BILIVERDINE IX ALPHA / type: ligand / ID: 2 / Number of copies: 2 / Formula: BLA
Molecular weightTheoretical: 582.646 Da
Chemical component information

ChemComp-BLA:
BILIVERDINE IX ALPHA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.37 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.7.1) / Number images used: 87111
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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