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Yorodumi- EMDB-39108: Pfr conformer of Arabidopsis thaliana phytochrome B in complex wi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39108 | |||||||||
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Title | Pfr conformer of Arabidopsis thaliana phytochrome B in complex with phytochrome-interacting factor 6 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | phytochrome / phytochrome interaction factor / signal complex / SIGNALING PROTEIN / GENE REGULATION | |||||||||
Function / homology | Function and homology information abscisic acid metabolic process / response to low fluence red light stimulus / red light photoreceptor activity / protein-phytochromobilin linkage / transpiration / red or far-red light signaling pathway / far-red light photoreceptor activity / red light signaling pathway / regulation of defense response / circadian regulation of calcium ion oscillation ...abscisic acid metabolic process / response to low fluence red light stimulus / red light photoreceptor activity / protein-phytochromobilin linkage / transpiration / red or far-red light signaling pathway / far-red light photoreceptor activity / red light signaling pathway / regulation of defense response / circadian regulation of calcium ion oscillation / response to low fluence blue light stimulus by blue low-fluence system / red or far-red light photoreceptor activity / regulation of photoperiodism, flowering / stomatal complex development / regulation of seed germination / gravitropism / jasmonic acid mediated signaling pathway / response to far red light / phototropism / photomorphogenesis / entrainment of circadian clock / detection of visible light / response to abscisic acid / response to salt / response to temperature stimulus / phosphorelay sensor kinase activity / photosynthesis / response to cold / promoter-specific chromatin binding / chromatin organization / sequence-specific DNA binding / protein dimerization activity / nuclear body / nuclear speck / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Wang Z / Wang W / Zhao D / Song Y / Xu B / Zhao J / Wang J | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell / Year: 2024 Title: Light-induced remodeling of phytochrome B enables signal transduction by phytochrome-interacting factor. Authors: Zhengdong Wang / Wenfeng Wang / Didi Zhao / Yanping Song / Xiaoli Lin / Meng Shen / Cheng Chi / Bin Xu / Jun Zhao / Xing Wang Deng / Jizong Wang / Abstract: Phytochrome B (phyB) and phytochrome-interacting factors (PIFs) constitute a well-established signaling module critical for plants adapting to ambient light. However, mechanisms underlying phyB ...Phytochrome B (phyB) and phytochrome-interacting factors (PIFs) constitute a well-established signaling module critical for plants adapting to ambient light. However, mechanisms underlying phyB photoactivation and PIF binding for signal transduction remain elusive. Here, we report the cryo-electron microscopy (cryo-EM) structures of the photoactivated phyB or the constitutively active phyB mutant in complex with PIF6, revealing a similar trimer. The light-induced configuration switch of the chromophore drives a conformational transition of the nearby tongue signature within the phytochrome-specific (PHY) domain of phyB. The resulting α-helical PHY tongue further disrupts the head-to-tail dimer of phyB in the dark-adapted state. These structural remodelings of phyB facilitate the induced-fit recognition of PIF6, consequently stabilizing the N-terminal extension domain and a head-to-head dimer of activated phyB. Interestingly, the phyB dimer exhibits slight asymmetry, resulting in the binding of only one PIF6 molecule. Overall, our findings solve a key question with respect to how light-induced remodeling of phyB enables PIF signaling in phytochrome research. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39108.map.gz | 27.2 MB | EMDB map data format | |
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Header (meta data) | emd-39108-v30.xml emd-39108.xml | 22.4 KB 22.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_39108_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_39108.png | 77.3 KB | ||
Filedesc metadata | emd-39108.cif.gz | 7.3 KB | ||
Others | emd_39108_half_map_1.map.gz emd_39108_half_map_2.map.gz | 49 MB 49 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39108 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39108 | HTTPS FTP |
-Validation report
Summary document | emd_39108_validation.pdf.gz | 1004.4 KB | Display | EMDB validaton report |
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Full document | emd_39108_full_validation.pdf.gz | 1003.9 KB | Display | |
Data in XML | emd_39108_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | emd_39108_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39108 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39108 | HTTPS FTP |
-Related structure data
Related structure data | 8yb4MC 9iuzC 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_39108.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_39108_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_39108_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of AtphyB-Pfr homodimer with AtPIF6
Entire | Name: Ternary complex of AtphyB-Pfr homodimer with AtPIF6 |
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Components |
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-Supramolecule #1: Ternary complex of AtphyB-Pfr homodimer with AtPIF6
Supramolecule | Name: Ternary complex of AtphyB-Pfr homodimer with AtPIF6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 120 KDa |
-Supramolecule #2: complex of AtphyB-Pfr homodimer
Supramolecule | Name: complex of AtphyB-Pfr homodimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
-Supramolecule #3: PIF6 monomer
Supramolecule | Name: PIF6 monomer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: phytochrome B
Macromolecule | Name: phytochrome B / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 129.8845 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: GPLGSMVSGV GGSGGGRGGG RGGEEEPSSS HTPNNRRGGE QAQSSGTKSL RPRSNTESMS KAIQQYTVDA RLHAVFEQSG ESGKSFDYS QSLKTTTYGS SVPEQQITAY LSRIQRGGYI QPFGCMIAVD ESSFRIIGYS ENAREMLGIM PQSVPTLEKP E ILAMGTDV ...String: GPLGSMVSGV GGSGGGRGGG RGGEEEPSSS HTPNNRRGGE QAQSSGTKSL RPRSNTESMS KAIQQYTVDA RLHAVFEQSG ESGKSFDYS QSLKTTTYGS SVPEQQITAY LSRIQRGGYI QPFGCMIAVD ESSFRIIGYS ENAREMLGIM PQSVPTLEKP E ILAMGTDV RSLFTSSSSI LLERAFVARE ITLLNPVWIH SKNTGKPFYA ILHRIDVGVV IDLEPARTED PALSIAGAVQ SQ KLAVRAI SQLQALPGGD IKLLCDTVVE SVRDLTGYDR VMVYKFHEDE HGEVVAESKR DDLEPYIGLH YPATDIPQAS RFL FKQNRV RMIVDCNATP VLVVQDDRLT QSMCLVGSTL RAPHGCHSQY MANMGSIASL AMAVIINGNE DDGSNVASGR SSMR LWGLV VCHHTSSRCI PFPLRYACEF LMQAFGLQLN MELQLALQMS EKRVLRTQTL LCDMLLRDSP AGIVTQSPSI MDLVK CDGA AFLYHGKYYP LGVAPSEVQI KDVVEWLLAN HADSTGLSTD SLGDAGYPGA AALGDAVCGM AVAYITKRDF LFWFRS HTA KEIKWGGAKH HPEDKDDGQR MHPRSSFQAF LEVVKSRSQP WETAEMDAIH SLQLILRDSF KESEAAMNSK VVDGVVQ PC RDMAGEQGID ELGAVAREMV RLIETATVPI FAVDAGGCIN GWNAKIAELT GLSVEEAMGK SLVSDLIYKE NEATVNKL L SRALRGDEEK NVEVKLKTFS PELQGKAVFV VVNACSSKDY LNNIVGVCFV GQDVTSQKIV MDKFINIQGD YKAIVHSPN PLIPPIFAAD ENTCCLEWNM AMEKLTGWSR SEVIGKMIVG EVFGSCCMLK GPDALTKFMI VLHNAIGGQD TDKFPFPFFD RNGKFVQAL LTANKRVSLE GKVIGAFCFL QIPSPELQQA LAVQRRQDTE CFTKAKELAY ICQVIKNPLS GMRFANSLLE A TDLNEDQK QLLETSVSCE KQISRIVGDM DLESIEDGSF VLKREEFFLG SVINAIVSQA MFLLRDRGLQ LIRDIPEEIK SI EVFGDQI RIQQLLAEFL LSIIRYAPSQ EWVEIHLSQL SKQMADGFAA IRTEFRMACP GEGLPPELVR DMFHSSRWTS PEG LGLSVC RKILKLMNGE VQYIRESERS YFLIILELPV PRKRPLSTAS GSGDMMLMMP Y UniProtKB: Phytochrome B |
-Macromolecule #2: phytochrome-interacting factor 6
Macromolecule | Name: phytochrome-interacting factor 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 11.688068 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPLGSMMFLP TDYCCRLSDQ EYMELVFENG QILAKGQRSN VSLHNQRTKS IMDLYEAEYN EDFMKSIIHG GGGAITNLGD TQVVPQSHV AAAHETNMLE SNKHVD UniProtKB: Transcription factor PIF6 |
-Macromolecule #3: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydro...
Macromolecule | Name: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol- ...Name: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid type: ligand / ID: 3 / Number of copies: 2 / Formula: O6E |
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Molecular weight | Theoretical: 586.678 Da |
Chemical component information | ChemComp-O6E: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||
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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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.41 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||||
Output model | PDB-8yb4: |