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- EMDB-35415: Cryo-EM structure of Arabidopsis phytochrome A. -

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Basic information

Entry
Database: EMDB / ID: EMD-35415
TitleCryo-EM structure of Arabidopsis phytochrome A.
Map data
Sample
  • Complex: Phytochrome A
    • Protein or peptide: Phytochrome A
  • 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 / Pr state / GENE REGULATION
Function / homology
Function and homology information


response to continuous far red light stimulus by the high-irradiance response system / response to very low fluence red light stimulus / far-red light photoreceptor activity / red light signaling pathway / red or far-red light photoreceptor activity / gravitropism / phototropism / response to far red light / photomorphogenesis / detection of visible light ...response to continuous far red light stimulus by the high-irradiance response system / response to very low fluence red light stimulus / far-red light photoreceptor activity / red light signaling pathway / red or far-red light photoreceptor activity / gravitropism / phototropism / response to far red light / photomorphogenesis / detection of visible light / response to arsenic-containing substance / phosphorelay sensor kinase activity / response to cold / protein kinase activity / negative regulation of translation / nuclear speck / nuclear body / mRNA binding / regulation of DNA-templated transcription / protein homodimerization activity / identical protein binding / nucleus / cytoplasm
Similarity search - Function
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 / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region ...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 / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / 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 / 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 superfamily
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMa L / Zhou C / Wang J / Guan Z / Yin P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2023
Title: Plant phytochrome A in the Pr state assembles as an asymmetric dimer.
Authors: Jiao Wang / Chen Zhou / Zeyuan Guan / Qiang Wang / Jun Zhao / Lixia Wang / Liuqing Zhang / Delin Zhang / Xing Wang Deng / Ling Ma / Ping Yin /
History
DepositionFeb 17, 2023-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35415.png

Downloads & links

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Map

FileDownload / File: emd_35415.map.gz / Format: CCP4 / Size: 83.7 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 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. 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: 0.3
Minimum - Maximum-2.320383 - 3.7945974
Average (Standard dev.)0.0017875246 (±0.087624416)
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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Additional map: This map was 3.4 angstrom with improved HKRD domain

Fileemd_35415_additional_1.map
AnnotationThis map was 3.4 angstrom with improved HKRD domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35415_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35415_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Phytochrome A

EntireName: Phytochrome A
Components
  • Complex: Phytochrome A
    • Protein or peptide: Phytochrome A
  • 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: Phytochrome A

SupramoleculeName: Phytochrome A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Phytochrome A

MacromoleculeName: Phytochrome A / type: protein_or_peptide / ID: 1
Details: Author stated the additional map was 3.4 angstrom with improved HKRD domain.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 124.652773 KDa
Recombinant expressionOrganism: Arabidopsis (plant)
SequenceString: MSGSRPTQSS EGSRRSRHSA RIIAQTTVDA KLHADFEESG SSFDYSTSVR VTGPVVENQP PRSDKVTTTY LHHIQKGKLI QPFGCLLAL DEKTFKVIAY SENASELLTM ASHAVPSVGE HPVLGIGTDI RSLFTAPSAS ALQKALGFGD VSLLNPILVH C RTSAKPFY ...String:
MSGSRPTQSS EGSRRSRHSA RIIAQTTVDA KLHADFEESG SSFDYSTSVR VTGPVVENQP PRSDKVTTTY LHHIQKGKLI QPFGCLLAL DEKTFKVIAY SENASELLTM ASHAVPSVGE HPVLGIGTDI RSLFTAPSAS ALQKALGFGD VSLLNPILVH C RTSAKPFY AIIHRVTGSI IIDFEPVKPY EVPMTAAGAL QSYKLAAKAI TRLQSLPSGS MERLCDTMVQ EVFELTGYDR VM AYKFHED DHGEVVSEVT KPGLEPYLGL HYPATDIPQA ARFLFMKNKV RMIVDCNAKH ARVLQDEKLS FDLTLCGSTL RAP HSCHLQ YMANMDSIAS LVMAVVVNEE DGEGDAPDAT TQPQKRKRLW GLVVCHNTTP RFVPFPLRYA CEFLAQVFAI HVNK EVELD NQMVEKNILR TQTLLCDMLM RDAPLGIVSQ SPNIMDLVKC DGAALLYKDK IWKLGTTPSE FHLQEIASWL CEYHM DSTG LSTDSLHDAG FPRALSLGDS VCGMAAVRIS SKDMIFWFRS HTAGEVRWGG AKHDPDDRDD ARRMHPRSSF KAFLEV VKT RSLPWKDYEM DAIHSLQLIL RNAFKDSETT DVNTKVIYSK LNDLKIDGIQ ELEAVTSEMV RLIETATVPI LAVDSDG LV NGWNTKIAEL TGLSVDEAIG KHFLTLVEDS SVEIVKRMLE NALEGTEEQN VQFEIKTHLS RADAGPISLV VNACASRD L HENVVGVCFV AHDLTGQKTV MDKFTRIEGD YKAIIQNPNP LIPPIFGTDE FGWCTEWNPA MSKLTGLKRE EVIDKMLLG EVFGTQKSCC RLKNQEAFVN LGIVLNNAVT SQDPEKVSFA FFTRGGKYVE CLLCVSKKLD REGVVTGVFC FLQLASHELQ QALHVQRLA ERTAVKRLKA LAYIKRQIRN PLSGIMFTRK MIEGTELGPE QRRILQTSAL CQKQLSKILD DSDLESIIEG C LDLEMKEF TLNEVLTAST SQVMMKSNGK SVRITNETGE EVMSDTLYGD SIRLQQVLAD FMLMAVNFTP SGGQLTVSAS LR KDQLGRS VHLANLEIRL THTGAGIPEF LLNQMFGTEE DVSEEGLSLM VSRKLVKLMN GDVQYLRQAG KSSFIITAEL AAA NK

UniProtKB: Phytochrome A

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Macromolecule #2: 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: 2 / 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

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 2.2 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 498817
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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