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- EMDB-42450: Pr/Pfr heterodimer (hybrid) state of Stigmatella aurantiaca bacte... -

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Basic information

Entry
Database: EMDB / ID: EMD-42450
TitlePr/Pfr heterodimer (hybrid) state of Stigmatella aurantiaca bacteriophytochrome 2
Map dataPr/Pfr heterodimer (hybrid) state of Stigmatella aurantiaca bacteriophytochrome 2
Sample
  • Organelle or cellular component: Stigmatella aurantiaca bacteriophytochrome
    • Protein or peptide: Bacteriophytochrome (Light-regulated signal transduction histidine kinase)
  • Ligand: BILIVERDINE IX ALPHA
KeywordsRed light photoreceptor / two component system / SIGNALING PROTEIN
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / histidine kinase / phosphorelay sensor kinase activity / protein kinase activator activity / photoreceptor activity / regulation of DNA-templated transcription
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. / Signal transduction histidine kinase, dimerisation/phosphoacceptor 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. / 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: 3.75 Å
AuthorsMalla TN / Schmidt M / Stojkovic EA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-STC-1231306 United States
National Science Foundation (NSF, United States)NSF STC BioXFEL center award 6227 United States
CitationJournal: Sci Adv / Year: 2024
Title: Photoreception and signaling in bacterial phytochrome revealed by single-particle cryo-EM.
Authors: Tek Narsingh Malla / Carolina Hernandez / Srinivasan Muniyappan / David Menendez / Dorina Bizhga / Joshua H Mendez / Peter Schwander / Emina A Stojković / Marius Schmidt /
Abstract: Phytochromes are red-light photoreceptors discovered in plants with homologs in bacteria and fungi that regulate a variety of physiological responses. They display a reversible photocycle between two ...Phytochromes are red-light photoreceptors discovered in plants with homologs in bacteria and fungi that regulate a variety of physiological responses. They display a reversible photocycle between two distinct states: a red-light-absorbing Pr state and a far-red light-absorbing Pfr state. The photoconversion regulates the activity of an enzymatic domain, usually a histidine kinase (HK). The molecular mechanism that explains how light controls the HK activity is not understood because structures of unmodified bacterial phytochromes with HK activity are missing. Here, we report three cryo-electron microscopy structures of a wild-type bacterial phytochrome with HK activity determined as Pr and Pfr homodimers and as a Pr/Pfr heterodimer with individual subunits in distinct states. We propose that the Pr/Pfr heterodimer is a physiologically relevant signal transduction intermediate. Our results offer insight into the molecular mechanism that controls the enzymatic activity of the HK as part of a bacterial two-component system that perceives and transduces light signals.
History
DepositionOct 22, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42450.png

Downloads & links

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Map

FileDownload / File: emd_42450.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPr/Pfr heterodimer (hybrid) state of Stigmatella aurantiaca bacteriophytochrome 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 303.84 Å		0.84 Å/pix.
x 360 pix.
= 303.84 Å		0.84 Å/pix.
x 360 pix.
= 303.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.1288981 - 0.31579986
Average (Standard dev.)0.00006705899 (±0.007447557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 303.84 Å
α=β=γ: 90.0 °

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Supplemental data

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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 (Light-regulated signal transduction histidine kinase)
  • 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)

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Macromolecule #1: Bacteriophytochrome (Light-regulated signal transduction histidin...

MacromoleculeName: Bacteriophytochrome (Light-regulated signal transduction histidine kinase)
type: protein_or_peptide / ID: 1
Details: The amino acids beyond residue number 536 were only interpreted with protein backbone including atom C-beta. With the resolution of the map near these residues, the backbone can be ...Details: The amino acids beyond residue number 536 were only interpreted with protein backbone including atom C-beta. With the resolution of the map near these residues, the backbone can be distinguished but the side chains are not resolved.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stigmatella aurantiaca (bacteria)
Molecular weightTheoretical: 81.150758 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRPSVSELEL SQCDREPIHL LGGIQAYGVL LAFRGPDRRL EVVSANTQAL LGRPPEALLG KTAAQVLPAE LWAQWELLSA RGALRVALP SGPYRALLHE SDGLTVLELE PAELQPDMEE TALELVRRLV SPLAGAKGTR ELLQTAANTV RALTGFDRVM V YRFDADWH ...String:
MRPSVSELEL SQCDREPIHL LGGIQAYGVL LAFRGPDRRL EVVSANTQAL LGRPPEALLG KTAAQVLPAE LWAQWELLSA RGALRVALP SGPYRALLHE SDGLTVLELE PAELQPDMEE TALELVRRLV SPLAGAKGTR ELLQTAANTV RALTGFDRVM V YRFDADWH GEVLAESKRE GMDGFLGMHF PATDIPVQAR ALYTRNPLRL IANARARPVP LVPSVVPELG RPLDLSGSAL RS VSPIHLE YLRNMGVEAS FSLSLLKDGA LWGLIACHHL APLHLSYERR RACEVLTQLL ALQLSSEERA AEAAEDSHRA ALL GPLATS LGAGGTLEEA LAKDGARVLE LTGATGAALL LGGEPLLVGR TPSMDEVEAL AAWLAPQPFQ TSFHTERLGS LYPP LAARA DVAAGLLAVR LAPASSRLAL WFRPEAVRTI SWAGNPRKPA EPEPGHARLH PRGSFQAWEE TVRETSPAWK RADLA AAEG FRSALIGVVL RQAAELERLS EALSRSNAEL DAFGHTVAHD LKEPLRGIQQ YAGFVMEDYH GALGPEGRGH MESLMW LAQ RSGDMLDGLF EYSRAGRVDL AWGEVNMQEV VDEVLATLST RFQAEKLTVR MPRRLPTVRC DGIRIAQVWA NLLVNAA KY QEGPERWVEA GFHGPGEPRP GAAGRYASAY VFYVKDPGIG IAPPFHEAIF EMFRRLHSAK AYGGGTGVGL AIARRLVQ L HGGALWVDSA PKQGATFYFT LGRGPG

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 stateparticle

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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 BIOQUANTUM (6k x 4k) / Average electron dose: 67.02 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 215374
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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