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- PDB-8yb4: Pfr conformer of Arabidopsis thaliana phytochrome B in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8yb4
TitlePfr conformer of Arabidopsis thaliana phytochrome B in complex with phytochrome-interacting factor 6
Components
  • phytochrome B
  • phytochrome-interacting factor 6
KeywordsGENE REGULATION / phytochrome / phytochrome interaction factor / signal complex / SIGNALING PROTEIN
Function / homology
Function and homology information


abscisic acid metabolic process / response to low fluence red light stimulus / red light photoreceptor activity / protein-phytochromobilin linkage / red or far-red light signaling pathway / transpiration / 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 / red or far-red light signaling pathway / transpiration / 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 / response to far red light / phototropism / photomorphogenesis / detection of visible light / entrainment of circadian clock / 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
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 / Histidine kinase-like ATPases / PAS domain superfamily / 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: 3.1 Å
AuthorsWang, Z. / Wang, W. / Zhao, D. / Song, Y. / Xu, B. / Zhao, J. / Wang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271253 China
CitationJournal: 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
DepositionFeb 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: phytochrome B
A: phytochrome B
C: phytochrome-interacting factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,6305
Polymers271,4573
Non-polymers1,1732
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 129884.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHYB, HY3, OOP1, At2g18790, MSF3.17 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14713
#2: Protein phytochrome-interacting factor 6 / PIF6 / Transcription factor PIF6 / Basic helix-loop-helix protein 132 / AtbHLH132 / bHLH 132 / ...PIF6 / Transcription factor PIF6 / Basic helix-loop-helix protein 132 / AtbHLH132 / bHLH 132 / Phytochrome interacting factor 3-like 2 / Transcription factor EN 111 / bHLH transcription factor bHLH132


Mass: 11688.068 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 (E. coli) / 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

Component
IDNameTypeEntity IDParent-IDSource
1Ternary complex of AtphyB-Pfr homodimer with AtPIF6COMPLEX#1-#20RECOMBINANT
2complex of AtphyB-Pfr homodimerCOMPLEX#11RECOMBINANT
3PIF6 monomerCOMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.26 MDaYES
210.25 MDaYES
310.12 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Arabidopsis thaliana (thale cress)3702
32Arabidopsis thaliana (thale cress)3702
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Escherichia coli (E. coli)562
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mmol/LtrisC4H11NO31
2150 mmol/Lsodium chlorideNaCl1
32 mL/100mLglycerolC3H8O31
42 mmol/LdithiothreitolC4H10O2S21
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.41 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.2particle selection
2EPU2.14image acquisition
4cryoSPARC4.1.2CTF correction
7UCSF ChimeraX1.7.1model fitting
8Coot0.9.8.7model fitting
10RELION4.0.0initial Euler assignment
11cryoSPARC4.1.2final Euler assignment
12RELION4.0.0classification
13cryoSPARC4.1.23D reconstruction
20PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 325483 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: AlphaFold / Type: in silico model

IDAccession codeChain-IDChain residue rangeInitial refinement model-ID
1AF-P14713-F1A49-6261
2AF-P14713-F1B100-6261
3AF-Q8L5W7-F1C15-672
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028607
ELECTRON MICROSCOPYf_angle_d0.56511646
ELECTRON MICROSCOPYf_dihedral_angle_d4.5151194
ELECTRON MICROSCOPYf_chiral_restr0.0391300
ELECTRON MICROSCOPYf_plane_restr0.0041506

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