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- EMDB-15685: Cryo-EM structure of DrBphP in Pr state -

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Basic information

Entry
Database: EMDB / ID: EMD-15685
TitleCryo-EM structure of DrBphP in Pr state
Map data
Sample
  • Complex: Full-length bacteriophytochrome fused to its response regulator from Deinococcus radiodurans.
    • Protein or peptide: Bacteriophytochrome,Response regulator
  • 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
KeywordsKINASE / PHOTOSENSOR / TRANSFERASE / PHYTOCHROME
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / photoreceptor activity / regulation of DNA-templated transcription / ATP binding ...osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
: / : / 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-related protein, C-terminal ...: / : / 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-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / 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 / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Bacteriophytochrome / Response regulator
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsWahlgren WY / Takala H / Westenhoff S
Funding supportEuropean Union, Finland, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)725642European Union
Academy of Finland330678 Finland
CitationJournal: Nat Commun / Year: 2022
Title: Structural mechanism of signal transduction in a phytochrome histidine kinase.
Authors: Weixiao Yuan Wahlgren / Elin Claesson / Iida Tuure / Sergio Trillo-Muyo / Szabolcs Bódizs / Janne A Ihalainen / Heikki Takala / Sebastian Westenhoff /
Abstract: Phytochrome proteins detect red/far-red light to guide the growth, motion, development and reproduction in plants, fungi, and bacteria. Bacterial phytochromes commonly function as an entrance signal ...Phytochrome proteins detect red/far-red light to guide the growth, motion, development and reproduction in plants, fungi, and bacteria. Bacterial phytochromes commonly function as an entrance signal in two-component sensory systems. Despite the availability of three-dimensional structures of phytochromes and other two-component proteins, the conformational changes, which lead to activation of the protein, are not understood. We reveal cryo electron microscopy structures of the complete phytochrome from Deinoccocus radiodurans in its resting and photoactivated states at 3.6 Å and 3.5 Å resolution, respectively. Upon photoactivation, the photosensory core module hardly changes its tertiary domain arrangement, but the connector helices between the photosensory and the histidine kinase modules open up like a zipper, causing asymmetry and disorder in the effector domains. The structures provide a framework for atom-scale understanding of signaling in phytochromes, visualize allosteric communication over several nanometers, and suggest that disorder in the dimeric arrangement of the effector domains is important for phosphatase activity in a two-component system. The results have implications for the development of optogenetic applications.
History
DepositionAug 27, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15685.png

Downloads & links

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Map

FileDownload / File: emd_15685.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 448 pix.
= 386.042 Å		0.86 Å/pix.
x 448 pix.
= 386.042 Å		0.86 Å/pix.
x 448 pix.
= 386.042 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8617 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.095
Minimum - Maximum-0.41377938 - 0.8432141
Average (Standard dev.)0.00014015874 (±0.011925108)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 386.0416 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15685_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15685_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15685_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Full-length bacteriophytochrome fused to its response regulator f...

EntireName: Full-length bacteriophytochrome fused to its response regulator from Deinococcus radiodurans.
Components
  • Complex: Full-length bacteriophytochrome fused to its response regulator from Deinococcus radiodurans.
    • Protein or peptide: Bacteriophytochrome,Response regulator
  • 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: Full-length bacteriophytochrome fused to its response regulator f...

SupramoleculeName: Full-length bacteriophytochrome fused to its response regulator from Deinococcus radiodurans.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant)
Molecular weightTheoretical: 101 KDa

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Macromolecule #1: Bacteriophytochrome,Response regulator

MacromoleculeName: Bacteriophytochrome,Response regulator / type: protein_or_peptide / ID: 1
Details: Sample is a fusion of Deinococcus radiodurans DrBphP and its response regulator DrRR.,Sample is a fusion of Deinococcus radiodurans DrBphP and its response regulator DrRR.
Number of copies: 2 / Enantiomer: LEVO / EC number: histidine kinase
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Molecular weightTheoretical: 101.579164 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASMTGGQQM GRGSMSRDPL PFFPPLYLGG PEITTENCER EPIHIPGSIQ PHGALLTADG HSGEVLQMSL NAATFLGQEP TVLRGQTLA ALLPEQWPAL QAALPPGCPD ALQYRATLDW PAAGHLSLTV HRVGELLILE FEPTEAWDST GPHALRNAMF A LESAPNLR ...String:
MASMTGGQQM GRGSMSRDPL PFFPPLYLGG PEITTENCER EPIHIPGSIQ PHGALLTADG HSGEVLQMSL NAATFLGQEP TVLRGQTLA ALLPEQWPAL QAALPPGCPD ALQYRATLDW PAAGHLSLTV HRVGELLILE FEPTEAWDST GPHALRNAMF A LESAPNLR ALAEVATQTV RELTGFDRVM LYKFAPDATG EVIAEARREG LHAFLGHRFP ASDIPAQARA LYTRHLLRLT AD TRAAAVP LDPVLNPQTN APTPLGGAVL RATSPMHMQY LRNMGVGSSL SVSVVVGGQL WGLIACHHQT PYVLPPDLRT TLE YLGRLL SLQVQVKEAA DVAAFRQSLR EHHARVALAA AHSLSPHDTL SDPALDLLGL MRAGGLILRF EGRWQTLGEV PPAP AVDAL LAWLETQPGA LVQTDALGQL WPAGADLAPS AAGLLAISVG EGWSECLVWL RPELRLEVAW GGATPDQAKD DLGPR HSFD TYLEEKRGYA EPWHPGEIEE AQDLRDTLTG ALGERLSVIR DLNRALTQSN AEWRQYGFVI SHHMQEPVRL ISQFAE LLT RQPRAQDGSP DSPQTERITG FLLRETSRLR SLTQDLHTYT ALLSAPPPVR RPTPLGRVVD DVLQDLEPRI ADTGASI EV APELPVIAAD AGLLRDLLLH LIGNALTFGG PEPRIAVRTE RQGAGWSIAV SDQGAGIAPE YQERIFLLFQ RLGSLDEA L GNGLGLPLCR KIAELHGGTL TVESAPGEGS TFRCWLPDAG PLPGAADAAS SAGGSAGSAG MPERASVPLR LLLVEDNAA DIFLMEMALE YSSVHTELLV ARDGLEALEL LEQAKTGGPF PDLILLDLNM PRVDGFELLQ ALRADPHLAH LPAIVLTTSN DPSDVKRAY ALQANSYLTK PSTLEDFLQL IERLTAYWFG TAAIPQTYQP QLEHHHHHH

UniProtKB: Bacteriophytochrome, Response regulator

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 117297
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4q0j


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8avw:
Cryo-EM structure of DrBphP in Pr state

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