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- EMDB-60816: Cryo-EM structure of PhyB(Y276H,1-908)-PIF6beta complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60816
TitleCryo-EM structure of PhyB(Y276H,1-908)-PIF6beta complex
Map data
Sample
  • Complex: PhyB(Y276H,1-908)-PIF6beta complex
    • Protein or peptide: Phytochrome B
    • Protein or peptide: Transcription factor PIF6
  • Ligand: 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
KeywordsPIF6-mediated / red light / signal transduction / phytochrome B / 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 / regulation of defense response / far-red light photoreceptor activity / red light signaling pathway / 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 / regulation of defense response / far-red light photoreceptor activity / red light signaling pathway / 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 / phototropism / response to far red light / photomorphogenesis / response to abscisic acid / entrainment of circadian clock / detection of visible light / response to salt / response to temperature stimulus / phosphorelay sensor kinase activity / response to light stimulus / 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
Transcription factor PIF3-like / : / Phytochrome A/B/C/D/E-like, histidine-kinase-related domain / Phytochrome A/B/C/D/E / Phytochrome chromophore binding site / Phytochrome chromophore attachment site signature. / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold ...Transcription factor PIF3-like / : / Phytochrome A/B/C/D/E-like, histidine-kinase-related domain / Phytochrome A/B/C/D/E / Phytochrome chromophore binding site / Phytochrome chromophore attachment site signature. / 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. / Helix-loop-helix DNA-binding domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Phytochrome B / Transcription factor PIF6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsJia HL / Guan ZY / Ding JY / Wang XY / Ma L / Yin P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2025
Title: Structural insight into PIF6-mediated red light signal transduction of plant phytochrome B.
Authors: Hanli Jia / Zeyuan Guan / Junya Ding / Xiaoyu Wang / Dingfang Tian / Yan Zhu / Delin Zhang / Zhu Liu / Ling Ma / Ping Yin /
Abstract: The red/far-red light receptor phytochrome B (phyB) plays essential roles in regulating various plant development processes. PhyB exists in two distinct photoreversible forms: the inactive Pr form ...The red/far-red light receptor phytochrome B (phyB) plays essential roles in regulating various plant development processes. PhyB exists in two distinct photoreversible forms: the inactive Pr form and the active Pfr form. phyB-Pfr binds phytochrome-interacting factors (PIFs) to transduce red light signals. Here, we determined the cryo-electron microscopy (cryo-EM) structures of the photoactivated phyB-Pfr‒PIF6 complex, the constitutively active mutant phyB‒PIF6 complex, and the truncated phyBN‒PIF6 complex. In these structures, two parallel phyB-Pfr molecules interact with one PIF6 molecule. Red light-triggered rotation of the PΦB D-ring leads to the conversion of hairpin loops into α helices and the "head-to-head" reassembly of phyB-Pfr N-terminal photosensory modules. The interaction between phyB-Pfr and PIF6 influences the dimerization and transcriptional activation activity of PIF6, and PIF6 stabilizes the N-terminal extension of phyB-Pfr and increases the Pr→Pfr photoconversion efficiency of phyB. Our findings reveal the molecular mechanisms underlying Pr→Pfr photoconversion and PIF6-mediated red light signal transduction of phyB.
History
DepositionJul 16, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60816.png

Downloads & links

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Map

FileDownload / File: emd_60816.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-2.9595256 - 4.4455433
Average (Standard dev.)0.00011528505 (±0.10236788)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60816_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

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Half map: #1

Fileemd_60816_half_map_2.map
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Sample components

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Entire : PhyB(Y276H,1-908)-PIF6beta complex

EntireName: PhyB(Y276H,1-908)-PIF6beta complex
Components
  • Complex: PhyB(Y276H,1-908)-PIF6beta complex
    • Protein or peptide: Phytochrome B
    • Protein or peptide: Transcription factor PIF6
  • Ligand: 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

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Supramolecule #1: PhyB(Y276H,1-908)-PIF6beta complex

SupramoleculeName: PhyB(Y276H,1-908)-PIF6beta complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Phytochrome B

MacromoleculeName: Phytochrome B / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 99.266367 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVSGVGGSGG GRGGGRGGEE EPSSSHTPNN RRGGEQAQSS GTKSLRPRSN TESMSKAIQQ YTVDARLHAV FEQSGESGKS FDYSQSLKT TTYGSSVPEQ QITAYLSRIQ RGGYIQPFGC MIAVDESSFR IIGYSENARE MLGIMPQSVP TLEKPEILAM G TDVRSLFT ...String:
MVSGVGGSGG GRGGGRGGEE EPSSSHTPNN RRGGEQAQSS GTKSLRPRSN TESMSKAIQQ YTVDARLHAV FEQSGESGKS FDYSQSLKT TTYGSSVPEQ QITAYLSRIQ RGGYIQPFGC MIAVDESSFR IIGYSENARE MLGIMPQSVP TLEKPEILAM G TDVRSLFT SSSSILLERA FVAREITLLN PVWIHSKNTG KPFYAILHRI DVGVVIDLEP ARTEDPALSI AGAVQSQKLA VR AISQLQA LPGGDIKLLC DTVVESVRDL TGYDRVMVHK FHEDEHGEVV AESKRDDLEP YIGLHYPATD IPQASRFLFK QNR VRMIVD CNATPVLVVQ DDRLTQSMCL VGSTLRAPHG CHSQYMANMG SIASLAMAVI INGNEDDGSN VASGRSSMRL WGLV VCHHT SSRCIPFPLR YACEFLMQAF GLQLNMELQL ALQMSEKRVL RTQTLLCDML LRDSPAGIVT QSPSIMDLVK CDGAA FLYH GKYYPLGVAP SEVQIKDVVE WLLANHADST GLSTDSLGDA GYPGAAALGD AVCGMAVAYI TKRDFLFWFR SHTAKE IKW GGAKHHPEDK DDGQRMHPRS SFQAFLEVVK SRSQPWETAE MDAIHSLQLI LRDSFKESEA AMNSKVVDGV VQPCRDM AG EQGIDELGAV AREMVRLIET ATVPIFAVDA GGCINGWNAK IAELTGLSVE EAMGKSLVSD LIYKENEATV NKLLSRAL R GDEEKNVEVK LKTFSPELQG KAVFVVVNAC SSKDYLNNIV GVCFVGQDVT SQKIVMDKFI NIQGDYKAIV HSPNPLIPP IFAADENTCC LEWNMAMEKL TGWSRSEVIG KMIVGEVFGS CCMLKGPDAL TKFMIVLHNA IGGQDTDKFP FPFFDRNGKF VQALLTANK RVSLEGKVIG AFCFLQIP

UniProtKB: Phytochrome B

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Macromolecule #2: Transcription factor PIF6

MacromoleculeName: Transcription factor PIF6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 20.379676 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MMFLPTDYCC RLSDQEYMEL VFENGQILAK GQRSNVSLHN QRTKSIMDLY EAEYNEDFMK SIIHGGGGAI TNLGDTQVVP QSHVAAAHE TNMLESNKHV DDSETLKASS SKRMMVDYHN RKKIKFIPPD EQSVVADRSF KLGFDTSSVG FTEDSEGSMY L SSSLDDES DDARPQVPAR TRK

UniProtKB: Transcription factor PIF6

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Macromolecule #3: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydro...

MacromoleculeName: 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
Molecular weightTheoretical: 586.678 Da
Chemical component information

ChemComp-O6E:
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

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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

Concentration0.7 mg/mL
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 565463
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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