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- EMDB-35693: Pr conformer of Zea mays phytochrome A1 - ZmphyA1-Pr -

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Basic information

Entry
Database: EMDB / ID: EMD-35693
TitlePr conformer of Zea mays phytochrome A1 - ZmphyA1-Pr
Map data
Sample
  • Complex: Zea mays phytochrome A1 (ZmphyA1-Pr)
    • Protein or peptide: Phytochrome
  • 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
Keywordsmaize phytochrome A1 / Pr conformer / far-red light receptor / PLANT PROTEIN
Function / homology
Function and homology information


protein-tetrapyrrole linkage / red, far-red light phototransduction / detection of visible light / photoreceptor activity / regulation of DNA-templated transcription / protein homodimerization activity / nucleus
Similarity search - Function
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 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. / 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 / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress) / Zea mays (maize)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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_35693.png

Downloads & links

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Map

FileDownload / File: emd_35693.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.68871117 - 1.0865606
Average (Standard dev.)0.000072731025 (±0.020370146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35693_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_35693_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 : Zea mays phytochrome A1 (ZmphyA1-Pr)

EntireName: Zea mays phytochrome A1 (ZmphyA1-Pr)
Components
  • Complex: Zea mays phytochrome A1 (ZmphyA1-Pr)
    • Protein or peptide: Phytochrome
  • 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: Zea mays phytochrome A1 (ZmphyA1-Pr)

SupramoleculeName: Zea mays phytochrome A1 (ZmphyA1-Pr) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Phytochrome

MacromoleculeName: Phytochrome / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 124.72643 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MSSLRPAQSS SSSSRTRQSS QARILAQTTL DAELNAEYEE SGDSFDYSKL VEAQRSTPPE QQGRSGKVIA YLQHIQRGKL IQPFGCLLA LDEKSFRVIA FSENAPEMLT TVSHAVPNVD DPPKLGIGTN VRSLFTDPGA TALQKALGFA DVSLLNPILV Q CKTSGKPF ...String:
MSSLRPAQSS SSSSRTRQSS QARILAQTTL DAELNAEYEE SGDSFDYSKL VEAQRSTPPE QQGRSGKVIA YLQHIQRGKL IQPFGCLLA LDEKSFRVIA FSENAPEMLT TVSHAVPNVD DPPKLGIGTN VRSLFTDPGA TALQKALGFA DVSLLNPILV Q CKTSGKPF YAIVHRATGC LVVDFEPVKP TEFPATAAGA LQSYKLAAKA ISKIQSLPGG SMQALCNTVV KEVFDLTGYD RV MAYKFHE DEHGEVFAEI TKPGIEPYLG LHYPATDIPQ AARFLFMKNK VRMICDCRAR SVKIIEDEAL SIDISLCGST LRA PHSCHL QYMENMNSIA SLVMAVVVNE NEDDDEPESE QPPQQQKRKK LWGLIVCHHE SPRYVPFPLR YACEFLAQVF AVHV NKEFE LEKQIREKSI LRMQTMLSDM LFKESSPLSI VSGSPNIMDL VKCDGAALLY GDKVWRLQTA PTESQIRDIA FWLSE VHGD STGLSTDSLQ DAGYPGAASL GDMICGMAVA KITSKDILFW FRSHTAAEIK WGGAKHDPSD EDDSRRMHPR LSFKAF LEV VKMKSLPWSD YEMDAIHSLQ LILRGTLNDA LKPAQSSGLD NQIGDLKLDG LAELQAVTSE MVRLMETATV PILAVDG NG LVNGWNQKVA DLSGLRVDEA IGRHILTLVE DSSVPIVQRM LYLALQGREE KEVRFELKTH GSKRDDGPVI LVVNACAS R DMHDHVVGVC FVAQDMTVHK LVMDKFTRVE GDYRAIIHNP NPLIPPIFGA DQFGWCSEWN AAMTKLTGWH RDEVIDRML LGEVFDSSNA SCLLKSKDAF VRLCIIINSA LAGEEAEKAP IGFFDRDGKY IECLLSVNRK VNADGVVTGV FCFIHVPSDD LQHALHVQQ ASEQTALRRL KAFSYMRHAI DKPLSGMLYS RETLKGTDLD EEQMRQVRVA DNCHRQLNKI LADLDQDNIT D KSSCLDLD MAEFVLQDVV VSAVSQVLIG CQGKGIRVAC NLPERSMKQK VYGDGIRLQQ ILSDFLFVSV KFSPAGGSVD IS SKLTKNS IGENLHLIDF ELRIKHQGAG VPAEILSQMY GEDNREQSEE GLSLLVSRNL LRLMNGDIRH LREAGMSTFI LTA ELAAA

UniProtKB: Phytochrome

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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: 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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 229726
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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