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- PDB-9ys3: Pr-pr homodimer state of Stigmatella aurantiaca bacteriophytochrome 2 -

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Basic information

Entry
Database: PDB / ID: 9ys3
TitlePr-pr homodimer state of Stigmatella aurantiaca bacteriophytochrome 2
ComponentsBacteriophytochrome
KeywordsSIGNALING PROTEIN / Signal Transduction / Photoactivation
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
BILIVERDINE IX ALPHA / histidine kinase
Similarity search - Component
Biological speciesStigmatella aurantiaca (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.85 Å
AuthorsKarki, P. / Stojkovic, E.A. / Schmidt, M.
Funding support United States, 3items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,6654
Polymers160,4992
Non-polymers1,1652
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Bacteriophytochrome


Mass: 80249.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stigmatella aurantiaca (bacteria) / Gene: SAMN05444354_11920 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1H7ZJA8, histidine kinase
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Stigmatella aurantiaca bacteriophytochrome / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.081 MDa / Experimental value: NO
Source (natural)Organism: Stigmatella aurantiaca (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 45.47 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCV4.7.1particle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARCv4.7.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70908 / Symmetry type: POINT
RefinementHighest resolution: 5.85 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310370
ELECTRON MICROSCOPYf_angle_d0.72414206
ELECTRON MICROSCOPYf_dihedral_angle_d6.511636
ELECTRON MICROSCOPYf_chiral_restr0.0461631
ELECTRON MICROSCOPYf_plane_restr0.0061927

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