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- EMDB-53916: PrPfr hybrid state of the Pseudomonas aeruginosa bacteriophytochr... -

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Basic information

Entry
Database: EMDB / ID: EMD-53916
TitlePrPfr hybrid state of the Pseudomonas aeruginosa bacteriophytochrome / PaBphP
Map data
Sample
  • Complex: Photochromic heterodimerimer of the bacterial phytochrome PaBphP
    • Protein or peptide: Bacteriophytochrome
  • Ligand: 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid
KeywordsPhytochrome / Bacteriophytochrome / Photoreceptor / Histidine kinase / CYTOSOLIC 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 / ATP binding / identical protein binding
Similarity search - Function
Phytochrome / : / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain ...Phytochrome / : / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / 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 superfamily
Similarity search - Domain/homology
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: Biorxiv / Year: 2025
Title: Chemical mechanism of allosteric and asymmetric dark reversion in a bacterial phytochrome uncovered by cryo-EM.
Authors: Bodizs SA / Fischer ALM / Cervenak M / Prodhan S / Maj M / Westenhoff S
History
DepositionMay 27, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53916.png

Downloads & links

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Map

FileDownload / File: emd_53916.map.gz / Format: CCP4 / Size: 244.1 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 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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 18.0
Minimum - Maximum-53.038933 - 95.410870000000003
Average (Standard dev.)-0.00027775366 (±1.1529282)
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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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
    • Protein or peptide: Bacteriophytochrome
  • Ligand: 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid

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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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Macromolecule #1: Bacteriophytochrome

MacromoleculeName: Bacteriophytochrome / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: histidine kinase
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 81.023703 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MTSITPVTLA NCEDEPIHVP GAIQPHGALV TLRADGMVLA ASENIQALLG FVASPGSYLT QEQVGPEVLR MLEEGLTGNG PWSNSVETR IGEHLFDVIG HSYKEVFYLE FEIRTADTLS ITSFTLNAQR IIAQVQLHND TASLLSNVTD ELRRMTGYDR V MAYRFRHD ...String:
MTSITPVTLA NCEDEPIHVP GAIQPHGALV TLRADGMVLA ASENIQALLG FVASPGSYLT QEQVGPEVLR MLEEGLTGNG PWSNSVETR IGEHLFDVIG HSYKEVFYLE FEIRTADTLS ITSFTLNAQR IIAQVQLHND TASLLSNVTD ELRRMTGYDR V MAYRFRHD DSGEVVAESR REDLESYLGQ RYPASDIPAQ ARRLYIQNPI RLIADVAYTP MRVFPALNPE TNESFDLSYS VL RSVSPIH CEYLTNMGVR ASMSISIVVG GKLWGLFSCH HMSPKLIPYP VRMSFQIFSQ VCSAIVERLE QGRIAELLRV STE RRLALA RRARDADDLF GALAHPDDGI AALIPCDGAL VMLGGRTLSI RGDFERQAGN VLQRLQRDPE RDIYHTDNWP QPSE DSPDG GDCCGVLAIR FHRQESGWIF WFRHEEVHRI RWGGKPEKLL TIGPSGPRLT PRGSFEAWEE VVRGHSTPWS ETDLA IAEK LRLDLMELCL NHAAEVDRMR QRLIAVLGHD LRNPLQSISM AAALLSSSDT RTTELRQHIS ASSSRMERLV SQILDM SRL QSGIGLTVNP VDTDVSQLVR QIVCETDVAY PGLVIEIAID PQVRAVVDPD RYAQVAANLL SNARHHGLPG RPVLVTL TR QGDEVCLSVL NETSGLSEAQ LANLFEPFKR ESADNQRNRN GLGIGLYISQ AIAQAHQGRI DVDCRDDVIT FCLRLPVR Q AETGSSS

UniProtKB: Bacteriophytochrome

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Macromolecule #2: 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidan...

MacromoleculeName: 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene- ...Name: 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid
type: ligand / ID: 2 / Number of copies: 2 / Formula: LBV
Molecular weightTheoretical: 585.67 Da

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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 reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.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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