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- EMDB-28872: CryoEM structure of Arabidopsis thaliana phytochrome A (focused m... -
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Open data
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Basic information
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Title | CryoEM structure of Arabidopsis thaliana phytochrome A (focused map of HKRD) | |||||||||
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![]() | Phytochrome / asymmetric dimer / gene regulation | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Li H | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The structure of Arabidopsis phytochrome A reveals topological and functional diversification among the plant photoreceptor isoforms. Authors: E Sethe Burgie / Hua Li / Zira T K Gannam / Katrice E McLoughlin / Richard D Vierstra / Huilin Li / ![]() Abstract: Plants employ a divergent cohort of phytochrome (Phy) photoreceptors to govern many aspects of morphogenesis through reversible photointerconversion between inactive Pr and active Pfr conformers. The ...Plants employ a divergent cohort of phytochrome (Phy) photoreceptors to govern many aspects of morphogenesis through reversible photointerconversion between inactive Pr and active Pfr conformers. The two most influential are PhyA whose retention of Pfr enables sensation of dim light, while the relative instability of Pfr for PhyB makes it better suited for detecting full sun and temperature. To better understand these contrasts, we solved, by cryo-electron microscopy, the three-dimensional structure of full-length PhyA as Pr. Like PhyB, PhyA dimerizes through head-to-head assembly of its C-terminal histidine kinase-related domains (HKRDs), while the remainder assembles as a head-to-tail light-responsive platform. Whereas the platform and HKRDs associate asymmetrically in PhyB dimers, these lopsided connections are absent in PhyA. Analysis of truncation and site-directed mutants revealed that this decoupling and altered platform assembly have functional consequences for Pfr stability of PhyA and highlights how plant Phy structural diversification has extended light and temperature perception. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.8 KB 18.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 130.3 KB | ||
Others | ![]() ![]() ![]() | 110.7 MB 116 MB 116 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_28872_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28872_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28872_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : phytochrome A
Entire | Name: phytochrome A |
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Components |
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-Supramolecule #1: phytochrome A
Supramolecule | Name: phytochrome A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 249 KDa |
-Macromolecule #1: phytochrome A
Macromolecule | Name: phytochrome A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: GMSGSRPTQS SEGSRRSRHS ARIIAQTTVD AKLHADFEES GSSFDYSTSV RVTGPVVENQ PPRSDKVTTT YLHHIQKGKL IQPFGCLLAL DEKTFKVIAY SENASELLTM ASHAVPSVGE HPVLGIGTDI RSLFTAPSAS ALQKALGFGD VSLLNPILVH CRTSAKPFYA ...String: GMSGSRPTQS SEGSRRSRHS ARIIAQTTVD AKLHADFEES GSSFDYSTSV RVTGPVVENQ PPRSDKVTTT YLHHIQKGKL IQPFGCLLAL DEKTFKVIAY SENASELLTM ASHAVPSVGE HPVLGIGTDI RSLFTAPSAS ALQKALGFGD VSLLNPILVH CRTSAKPFYA IIHRVTGSII IDFEPVKPYE VPMTAAGALQ SYKLAAKAIT RLQSLPSGSM ERLCDTMVQE VFELTGYDRV MAYKFHEDDH GEVVSEVTKP GLEPYLGLHY PATDIPQAAR FLFMKNKVRM IVDCNAKHAR VLQDEKLSFD LTLCGSTLRA PHSCHLQYMA NMDSIASLVM AVVVNEEDGE GDAPDATTQP QKRKRLWGLV VCHNTTPRFV PFPLRYACEF LAQVFAIHVN KEVELDNQMV EKNILRTQTL LCDMLMRDAP LGIVSQSPNI MDLVKCDGAA LLYKDKIWKL GTTPSEFHLQ EIASWLCEYH MDSTGLSTDS LHDAGFPRAL SLGDSVCGMA AVRISSKDMI FWFRSHTAGE VRWGGAKHDP DDRDDARRMH PRSSFKAFLE VVKTRSLPWK DYEMDAIHSL QLILRNAFKD SETTDVNTKV IYSKLNDLKI DGIQELEAVT SEMVRLIETA TVPILAVDSD GLVNGWNTKI AELTGLSVDE AIGKHFLTLV EDSSVEIVKR MLENALEGTE EQNVQFEIKT HLSRADAGPI SLVVNACASR DLHENVVGVC FVAHDLTGQK TVMDKFTRIE GDYKAIIQNP NPLIPPIFGT DEFGWCTEWN PAMSKLTGLK REEVIDKMLL GEVFGTQKSC CRLKNQEAFV NLGIVLNNAV TSQDPEKVSF AFFTRGGKYV ECLLCVSKKL DREGVVTGVF CFLQLASHEL QQALHVQRLA ERTAVKRLKA LAYIKRQIRN PLSGIMFTRK MIEGTELGPE QRRILQTSAL CQKQLSKILD DSDLESIIEG CLDLEMKEFT LNEVLTASTS QVMMKSNGKS VRITNETGEE VMSDTLYGDS IRLQQVLADF MLMAVNFTPS GGQLTVSASL RKDQLGRSVH LANLEIRLTH TGAGIPEFLL NQMFGTEEDV SEEGLSLMVS RKLVKLMNGD VQYLRQAGKS SFIITAELAA ANK |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.0 mg/mL | |||||||||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 299 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 193.0 K / Max: 193.0 K |
Alignment procedure | Coma free - Residual tilt: 0.05 mrad |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 6390 / Average exposure time: 1.0 sec. / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 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 |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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