Yorodumi
- EMDB-41942: Cryo-EM structure of PsBphP in Pfr state, Dimer of Dimers PSM only -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41942 | |||||||||
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Title | Cryo-EM structure of PsBphP in Pfr state, Dimer of Dimers PSM only | |||||||||
Map data | Cryo-EM map of PsBphP in Pfr state, Dimer of Dimers PSM only, post-processed with deepEMhancer | |||||||||
Sample |
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Keywords | Pseudomonas syringae bacteriophytochrome / PLANT PROTEIN | |||||||||
Function / homology | Function and homology information detection of visible light / histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription Similarity search - Function | |||||||||
Biological species | Pseudomonas syringae pv. tomato str. DC3000 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.01 Å | |||||||||
Authors | Basore K / Burgie ES / Vierstra D | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Signaling by a bacterial phytochrome histidine kinase involves a conformational cascade reorganizing the dimeric photoreceptor. Authors: E Sethe Burgie / Katherine Basore / Michael J Rau / Brock Summers / Alayna J Mickles / Vadim Grigura / James A J Fitzpatrick / Richard D Vierstra / Abstract: Phytochromes (Phys) are a divergent cohort of bili-proteins that detect light through reversible interconversion between dark-adapted Pr and photoactivated Pfr states. While our understandings of ...Phytochromes (Phys) are a divergent cohort of bili-proteins that detect light through reversible interconversion between dark-adapted Pr and photoactivated Pfr states. While our understandings of downstream events are emerging, it remains unclear how Phys translate light into an interpretable conformational signal. Here, we present models of both states for a dimeric Phy with histidine kinase (HK) activity from the proteobacterium Pseudomonas syringae, which were built from high-resolution cryo-EM maps (2.8-3.4-Å) of the photosensory module (PSM) and its following signaling (S) helix together with lower resolution maps for the downstream output region augmented by RoseTTAFold and AlphaFold structural predictions. The head-to-head models reveal the PSM and its photointerconversion mechanism with strong clarity, while the HK region is interpretable but relatively mobile. Pr/Pfr comparisons show that bilin phototransformation alters PSM architecture culminating in a scissoring motion of the paired S-helices linking the PSMs to the HK bidomains that ends in reorientation of the paired catalytic ATPase modules relative to the phosphoacceptor histidines. This action apparently primes autophosphorylation enroute to phosphotransfer to the cognate DNA-binding response regulator AlgB which drives quorum-sensing behavior through transient association with the photoreceptor. Collectively, these models illustrate how light absorption conformationally translates into accelerated signaling by Phy-type kinases. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41942.map.gz | 416.3 MB | EMDB map data format | |
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Header (meta data) | emd-41942-v30.xml emd-41942.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41942_fsc.xml | 18.6 KB | Display | FSC data file |
Images | emd_41942.png | 101.8 KB | ||
Filedesc metadata | emd-41942.cif.gz | 6.6 KB | ||
Others | emd_41942_additional_1.map.gz emd_41942_half_map_1.map.gz emd_41942_half_map_2.map.gz | 237.2 MB 443.1 MB 443.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41942 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41942 | HTTPS FTP |
-Related structure data
Related structure data | 8u63MC 8u4xC 8u62C 8u64C 8u65C 8u8zC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41942.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of PsBphP in Pfr state, Dimer of Dimers PSM only, post-processed with deepEMhancer | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.657 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Cryo-EM map of PsBphP in Pfr state, Dimer...
File | emd_41942_additional_1.map | ||||||||||||
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Annotation | Cryo-EM map of PsBphP in Pfr state, Dimer of Dimers PSM only, unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM map of PsBphP in Pfr state, Dimer...
File | emd_41942_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM map of PsBphP in Pfr state, Dimer of Dimers PSM only, half-map #1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM map of PsBphP in Pfr state, Dimer...
File | emd_41942_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM map of PsBphP in Pfr state, Dimer of Dimers PSM only, half-map #2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PsBphP
Entire | Name: PsBphP |
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Components |
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-Supramolecule #1: PsBphP
Supramolecule | Name: PsBphP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Pseudomonas syringae pv. tomato str. DC3000 (bacteria) |
-Macromolecule #1: histidine kinase
Macromolecule | Name: histidine kinase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas syringae pv. tomato str. DC3000 (bacteria) |
Molecular weight | Theoretical: 82.382555 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GMSQLDKDAF EVLLANCADE PIQFPGAIQP HGLLFTLKEP ELTILQVSAN VQSVLGKVPD QLAGQTLDCV LGAGWAEVIR STSANDSLV DVPRLLMSVE GVEFEALLHR SQEALVLELE IQDKAAQAIS YSERTGNMGR MLRQLHAAAD LQTLYEVSVR E IQRMTGYD ...String: GMSQLDKDAF EVLLANCADE PIQFPGAIQP HGLLFTLKEP ELTILQVSAN VQSVLGKVPD QLAGQTLDCV LGAGWAEVIR STSANDSLV DVPRLLMSVE GVEFEALLHR SQEALVLELE IQDKAAQAIS YSERTGNMGR MLRQLHAAAD LQTLYEVSVR E IQRMTGYD RVLIYRFEEE GHGQVIAEAS APAMELFNGL FFPASDIPEQ ARELYRRNWL RIIPDANYTP VPLVPQLRPD TQ QQLDLSF STLRSVSPIH CQYMKNMGVL SSMSVSLIQG GKLWGLISCG HRTPLYVSHE LRSACQAIGQ VLSLQISAME ALE VSRQRE TKIQTLQQLH QMMATSDTDV FDGLAQQPQL LMDLVGATGV AIIEDRQTHC YGNCPEPSDI RALHTWMMAG GEPV YASHH LSSVYPPGEA YQTLASGVLA MSLPKPVDNG VIWFRPEVKQ SVQWSGDPNK PLNLDASDNT LRLQPRTSFE IWKVE MTGI ATKWSHGDVF AANDLRRSAL ENDLARQVSK EQQAVRARDE LVAVVSHDLR NPMTVISMLC GMMQKSFSSD GPHTSR RIS TAIDTMQQAA SRMNVLLEDL LDTSKIEAGR YTITPQPLEV SQIFEEAYTL LAPLAMDKSI EISFNAEPDI KVNADPE RL FQVLSNLIGN AIKFTPKLGR IGVAAMSNGD EVVFTVRDSG EGIPPEQLPH IFERYWTVKE GNPTGTGLGL YISQGIIK A HGGELAAQSQ VGHGSEFRFT VPIAH UniProtKB: histidine kinase |
-Macromolecule #2: 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidan...
Macromolecule | 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- ...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 |
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Molecular weight | Theoretical: 585.67 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 82.0 K / Max: 84.0 K |
Specialist optics | Spherical aberration corrector: Microscope is outfitted with a Cs image corrector with two hexapole elements. |
Details | Preliminary grid screening was performed manually. |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 3 / Number real images: 12593 / Average exposure time: 4.28 sec. / Average electron dose: 51.78 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 150.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |