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- EMDB-70119: Pr/Pr homodimer of Stigmatella aurantiaca bacteriophytochrome 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-70119
TitlePr/Pr homodimer of Stigmatella aurantiaca bacteriophytochrome 2
Map dataFull map
Sample
  • Organelle or cellular component: Stigmatella aurantiaca bacteriophytochrome
    • Protein or peptide: Bacteriophytochrome
KeywordsPhotoreceptor / Bacteriophytochrome / SIGNALING PROTEIN
Biological speciesStigmatella aurantiaca (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsKarki P / Stojkovic EA / Schmidt M
Funding support United States, 4 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-STC-1231306 United States
National Science Foundation (NSF, United States)6227 United States
Simons FoundationSF349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
CitationJournal: Struct Dyn / Year: 2025
Title: Structures of myxobacterial phytochrome revealed by cryo-EM using the Spotiton technique and with x-ray crystallography.
Authors: Prabin Karki / David Menendez / William Budell / Shishir Dangi / Carolina Hernandez / Joshua Mendez / Srinivasan Muniyappan / Shibom Basu / Peter Schwander / Tek N Malla / Emina A Stojković / Marius Schmidt /
Abstract: Phytochromes are red-light photoreceptors first identified in plants, with homologs found in bacteria and fungi, that regulate a variety of critical physiological processes. They undergo a reversible ...Phytochromes are red-light photoreceptors first identified in plants, with homologs found in bacteria and fungi, that regulate a variety of critical physiological processes. They undergo a reversible photocycle between two distinct states: a red-light-absorbing Pr form and a far-red light-absorbing Pfr form. This Pr/Pfr photoconversion controls the activity of a C-terminal enzymatic domain, typically a histidine kinase (HK). However, the molecular mechanisms underlying light-induced regulation of HK activity in bacteria remain poorly understood, as only a few structures of unmodified bacterial phytochromes with HK activity are known. Recently, cryo-EM structures of a wild-type bacterial phytochrome with HK activity are solved that reveal homodimers in both the Pr and Pfr states, as well as a heterodimer with individual monomers in distinct Pr and Pfr states. Cryo-EM structures of a truncated version of the same phytochrome-lacking the HK domain-also show a homodimer in the Pfr state and a Pr/Pfr heterodimer. Here, we describe in detail how structural information is obtained from cryo-EM data on a full-length intact bacteriophytochrome, and how the cryo-EM structure can contribute to the understanding of the function of the phytochrome. In addition, we compare the cryo-EM structure to an unusual x-ray structure that is obtained from a fragmented full-length phytochrome crystallized in the Pr-state.
History
DepositionApr 9, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70119.png

Downloads & links

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Map

FileDownload / File: emd_70119.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 216 pix.
= 358.128 Å		1.66 Å/pix.
x 216 pix.
= 358.128 Å		1.66 Å/pix.
x 216 pix.
= 358.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.658 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.171
Minimum - Maximum-0.83089566 - 1.5554789
Average (Standard dev.)-0.000498397 (±0.041415203)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 358.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_70119_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_70119_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

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Supramolecule #1: Stigmatella aurantiaca bacteriophytochrome

SupramoleculeName: Stigmatella aurantiaca bacteriophytochrome / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
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 / Enantiomer: LEVO
Source (natural)Organism: Stigmatella aurantiaca (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ELSQCDREPI HLLGGIQAYG VLLAFRGPDR RLEVVSANTQ ALLGRPPEAL LGKTAAQVLP AELWAQWELL SARGALRVAL PSGPYRALLH ESDGLTVLEL EPAELQPDME ETALELVRRL VSPLAGAKGT RELLQTAANT VRALTGFDRV MVYRFDADWH GEVLAESKRE ...String:
ELSQCDREPI HLLGGIQAYG VLLAFRGPDR RLEVVSANTQ ALLGRPPEAL LGKTAAQVLP AELWAQWELL SARGALRVAL PSGPYRALLH ESDGLTVLEL EPAELQPDME ETALELVRRL VSPLAGAKGT RELLQTAANT VRALTGFDRV MVYRFDADWH GEVLAESKRE GMDGFLGMHF PATDIPVQAR ALYTRNPLRL IANARARPVP LVPSVVPELG RPLDLSGSAL RSVSPIHLEY LRNMGVEASF SLSLLKDGAL WGLIACHHLA PLHLSYERRR ACEVLTQLLA LQLSSEERAA EAAEDSHRAA LLGPLATSLG AGGTLEEALA KDGARVLELT GATGAALLLG GEPLLVGRTP SMDEVEALAA WLAPQPFQTS FHTERLGSLY PPLAARADVA AGLLAVRLAP ASSRLALWFR PEAVRTISWA GNPRKPAEPE PGHARLHPRG SFQAWEETVR ETSPAWKRAD LAAAEGFRSA LIGVVLRQAA ELERLSEALS RSNAELDAFG HTVAHDLKEP LRGIQQYAGF VMEDYHGALG PEGRGHMESL MWLAQRSGDM LDGLFEYSRA GRVDLAWGEV NMQEVVDEVL ATLSTRFQAE KLTVRMPRRL PTVRCDGIRI AQVWANLLVN AAKYQEGPER WVEAGFHGPG EPRPGAAGRY ASAYVFYVKD PGIGIAPPFH EAIFEMFRRL HSAKAYGGGT GVGLAIARRL VQLHGGALWV DSAPKQGATF YFTLGRGPG

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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: 45.47 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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 (ver. 4.4.1) / Software - details: Patch CTF estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 229519
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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