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- PDB-9itf: Cryo-EM structure of full-length phyB(Y276H)-PIF6beta complex -

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Basic information

Entry
Database: PDB / ID: 9itf
TitleCryo-EM structure of full-length phyB(Y276H)-PIF6beta complex
Components
  • Phytochrome B
  • Transcription factor PIF6
KeywordsGENE REGULATION / PIF6-mediated / red light / signal transduction / phytochrome B
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 speck / nuclear body / 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
Chem-O6E / Phytochrome B / Transcription factor PIF6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsJia, H.L. / Guan, Z.Y. / Ding, J.Y. / Wang, X.Y. / Ma, L. / Yin, P.
Funding support China, 1items
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 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Phytochrome B
A: Phytochrome B
B: Transcription factor PIF6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,3895
Polymers298,2153
Non-polymers1,1732
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Phytochrome B / Protein LONG HYPOCOTYL 3 / Protein OUT OF PHASE 1


Mass: 135782.516 Da / Num. of mol.: 2 / Mutation: Y276H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHYB, HY3, OOP1, At2g18790, MSF3.17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14713
#2: Protein Transcription factor PIF6 / Basic helix-loop-helix protein 132 / AtbHLH132 / bHLH 132 / Phytochrome interacting factor 3-like 2 ...Basic helix-loop-helix protein 132 / AtbHLH132 / bHLH 132 / Phytochrome interacting factor 3-like 2 / Phytochrome-interacting factor 6 / Transcription factor EN 111 / bHLH transcription factor bHLH132


Mass: 26650.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PIF6, BHLH132, EN111, PIL2, At3g62090, T17J13.50 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8L5W7
#3: Chemical 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


Mass: 586.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H38N4O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PhyB(full length)-PIF6beta complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI SPIRIT
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 277480 / Symmetry type: POINT
RefinementHighest resolution: 2.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048082
ELECTRON MICROSCOPYf_angle_d1.19710926
ELECTRON MICROSCOPYf_dihedral_angle_d16.5791147
ELECTRON MICROSCOPYf_chiral_restr0.061232
ELECTRON MICROSCOPYf_plane_restr0.0051388

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