[English] 日本語
Yorodumi
- EMDB-60916: Constitutively active mutant(Y276H) of Arabidopsis phytochrome B(... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60916
TitleConstitutively active mutant(Y276H) of Arabidopsis phytochrome B(phyB) in complex with phytochrome-interacting factor 6(PIF6)
Map data
Sample
  • Complex: Ternary complex of phyB mutant(Y276H) with PIF6
    • Complex: complex of phyB mutant(Y276H) homodimer
      • Protein or peptide: Phytochrome B
    • Complex: PIF6 monomer
      • Protein or peptide: Phytochrome-interacting factor 6
  • 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
KeywordsPhytochrome / Phytochrome-interacting factor / Signal complex / 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 / 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 / response to light stimulus / photosynthesis / response to cold / promoter-specific chromatin binding / chromatin organization / sequence-specific DNA binding / nuclear body / protein dimerization activity / 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: 3.19 Å
AuthorsWang Z / Wang W / Zhao D / Song Y / Xu B / Zhao J / Wang J
Funding support China, 1 items
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
DepositionJul 22, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60916.png

Downloads & links

-
Map

FileDownload / File: emd_60916.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 240 pix.
= 204. Å		0.85 Å/pix.
x 240 pix.
= 204. Å		0.85 Å/pix.
x 240 pix.
= 204. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.093
Minimum - Maximum-0.42078573 - 0.7782485
Average (Standard dev.)0.0004990058 (±0.02157082)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 204.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_60916_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60916_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ternary complex of phyB mutant(Y276H) with PIF6

EntireName: Ternary complex of phyB mutant(Y276H) with PIF6
Components
  • Complex: Ternary complex of phyB mutant(Y276H) with PIF6
    • Complex: complex of phyB mutant(Y276H) homodimer
      • Protein or peptide: Phytochrome B
    • Complex: PIF6 monomer
      • Protein or peptide: Phytochrome-interacting factor 6
  • 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

-
Supramolecule #1: Ternary complex of phyB mutant(Y276H) with PIF6

SupramoleculeName: Ternary complex of phyB mutant(Y276H) with PIF6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 100 KDa

-
Supramolecule #2: complex of phyB mutant(Y276H) homodimer

SupramoleculeName: complex of phyB mutant(Y276H) homodimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

-
Supramolecule #3: PIF6 monomer

SupramoleculeName: PIF6 monomer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

-
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: 99.764898 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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 VMVHKFHEDE 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 QIPS

UniProtKB: Phytochrome B

-
Macromolecule #2: Phytochrome-interacting factor 6

MacromoleculeName: Phytochrome-interacting factor 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 11.688068 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
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...

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mmol/LC4H11NO3tris
150.0 mmol/LNaClsodium chloride
2.0 mL/100mLC3H8O3glycerol
2.0 mmol/LC4H10O2S2dithiothreitol
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.41 sec. / 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Details: Startup model was generated from particle images using CryoSPARC ab-initio reconstruction.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 366884
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.1.2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.1.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.1.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

8yb4

chain_id: A, residue_range: 111-621, source_name: PDB, initial_model_type: experimental model

8yb4

chain_id: B, residue_range: 53-621, source_name: PDB, initial_model_type: experimental model

8yb4

chain_id: C, residue_range: 10-60, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9iuz:
Constitutively active mutant(Y276H) of Arabidopsis phytochrome B(phyB) in complex with phytochrome-interacting factor 6(PIF6)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more