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- EMDB-35691: Photochromobilin-free form of Arabidopsis thaliana phytochrome A ... -

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Basic information

Entry
Database: EMDB / ID: EMD-35691
TitlePhotochromobilin-free form of Arabidopsis thaliana phytochrome A - apo-AtphyA
Map data
Sample
  • Complex: Photochromobilin-free form of Arabidopsis thaliana phytochrome A (apo-AtphyA)
    • Protein or peptide: Phytochrome A
Keywordsphytochrome A / Photochromobilin-free form / far-red light receptor / PLANT PROTEIN
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 / response to far red light / phototropism / 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 / response to far red light / phototropism / photomorphogenesis / detection of visible light / response to arsenic-containing substance / phosphorelay sensor kinase activity / response to cold / negative regulation of translation / nuclear body / protein kinase activity / nuclear speck / 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 / PAS fold-2 / PAS fold / Phytochrome, central region / 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 / PAS fold-2 / PAS fold / Phytochrome, central region / 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 / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.77 Å
AuthorsZhang Y / Ma C / Zhao J / Gao N / Wang J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2023
Title: Structural insights into plant phytochrome A as a highly sensitized photoreceptor.
Authors: Yuxuan Zhang / Xiaoli Lin / Chengying Ma / Jun Zhao / Xiaojin Shang / Zhengdong Wang / Bin Xu / Ning Gao / Xing Wang Deng / Jizong Wang /
History
DepositionMar 20, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35691.png

Downloads & links

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Map

FileDownload / File: emd_35691.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.03515247 - 0.050794084
Average (Standard dev.)0.00012227941 (±0.0013288)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #1

Fileemd_35691_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35691_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 : Photochromobilin-free form of Arabidopsis thaliana phytochrome A ...

EntireName: Photochromobilin-free form of Arabidopsis thaliana phytochrome A (apo-AtphyA)
Components
  • Complex: Photochromobilin-free form of Arabidopsis thaliana phytochrome A (apo-AtphyA)
    • Protein or peptide: Phytochrome A

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Supramolecule #1: Photochromobilin-free form of Arabidopsis thaliana phytochrome A ...

SupramoleculeName: Photochromobilin-free form of Arabidopsis thaliana phytochrome A (apo-AtphyA)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Phytochrome A

MacromoleculeName: Phytochrome A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 125.17143 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MEKKMSGSRP TQSSEGSRRS RHSARIIAQT TVDAKLHADF EESGSSFDYS TSVRVTGPVV ENQPPRSDKV TTTYLHHIQK GKLIQPFGC LLALDEKTFK VIAYSENASE LLTMASHAVP SVGEHPVLGI GTDIRSLFTA PSASALQKAL GFGDVSLLNP I LVHCRTSA ...String:
MEKKMSGSRP TQSSEGSRRS RHSARIIAQT TVDAKLHADF EESGSSFDYS TSVRVTGPVV ENQPPRSDKV TTTYLHHIQK GKLIQPFGC LLALDEKTFK VIAYSENASE LLTMASHAVP SVGEHPVLGI GTDIRSLFTA PSASALQKAL GFGDVSLLNP I LVHCRTSA KPFYAIIHRV TGSIIIDFEP VKPYEVPMTA AGALQSYKLA AKAITRLQSL PSGSMERLCD TMVQEVFELT GY DRVMAYK FHEDDHGEVV SEVTKPGLEP YLGLHYPATD IPQAARFLFM KNKVRMIVDC NAKHARVLQD EKLSFDLTLC GST LRAPHS CHLQYMANMD SIASLVMAVV VNEEDGEGDA PDATTQPQKR KRLWGLVVCH NTTPRFVPFP LRYACEFLAQ VFAI HVNKE VELDNQMVEK NILRTQTLLC DMLMRDAPLG IVSQSPNIMD LVKCDGAALL YKDKIWKLGT TPSEFHLQEI ASWLC EYHM DSTGLSTDSL HDAGFPRALS LGDSVCGMAA VRISSKDMIF WFRSHTAGEV RWGGAKHDPD DRDDARRMHP RSSFKA FLE VVKTRSLPWK DYEMDAIHSL QLILRNAFKD SETTDVNTKV IYSKLNDLKI DGIQELEAVT SEMVRLIETA TVPILAV DS DGLVNGWNTK IAELTGLSVD EAIGKHFLTL VEDSSVEIVK RMLENALEGT EEQNVQFEIK THLSRADAGP ISLVVNAC A SRDLHENVVG VCFVAHDLTG QKTVMDKFTR IEGDYKAIIQ NPNPLIPPIF GTDEFGWCTE WNPAMSKLTG LKREEVIDK MLLGEVFGTQ KSCCRLKNQE AFVNLGIVLN NAVTSQDPEK VSFAFFTRGG KYVECLLCVS KKLDREGVVT GVFCFLQLAS HELQQALHV QRLAERTAVK RLKALAYIKR QIRNPLSGIM FTRKMIEGTE LGPEQRRILQ TSALCQKQLS KILDDSDLES I IEGCLDLE MKEFTLNEVL TASTSQVMMK SNGKSVRITN ETGEEVMSDT LYGDSIRLQQ VLADFMLMAV NFTPSGGQLT VS ASLRKDQ LGRSVHLANL EIRLTHTGAG IPEFLLNQMF GTEEDVSEEG LSLMVSRKLV KLMNGDVQYL RQAGKSSFII TAE LAAANK

UniProtKB: Phytochrome A

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 873442

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