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- EMDB-73380: Pr-pr homodimer state of Stigmatella aurantiaca bacteriophytochrome 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-73380
TitlePr-pr homodimer 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: 5.85 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: To Be Published
Title: Pr-pr homodimer state of Stigmatella aurantiaca bacteriophytochrome 2
Authors: Karki P / Schmidt M
History
DepositionOct 17, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73380.png

Downloads & links

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Map

FileDownload / File: emd_73380.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 350 pix.
= 290.15 Å		0.83 Å/pix.
x 350 pix.
= 290.15 Å		0.83 Å/pix.
x 350 pix.
= 290.15 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0228
Minimum - Maximum-0.07409837 - 0.19880708
Average (Standard dev.)0.000203499 (±0.00718897)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 290.15 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73380_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73380_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73380_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 : 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: 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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.7.1) / Number images used: 70908
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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