+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35693 | |||||||||
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Title | Pr conformer of Zea mays phytochrome A1 - ZmphyA1-Pr | |||||||||
Map data | ||||||||||
Sample |
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Keywords | maize 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 | |||||||||
Biological species | Arabidopsis thaliana (thale cress) / Zea mays (maize) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Zhang Y / Ma C / Zhao J / Gao N / Wang J | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35693.map.gz | 64.2 MB | EMDB map data format | |
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Header (meta data) | emd-35693-v30.xml emd-35693.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
Images | emd_35693.png | 36.5 KB | ||
Filedesc metadata | emd-35693.cif.gz | 6.1 KB | ||
Others | emd_35693_half_map_1.map.gz emd_35693_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35693 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35693 | HTTPS FTP |
-Validation report
Summary document | emd_35693_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_35693_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_35693_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | emd_35693_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35693 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35693 | HTTPS FTP |
-Related structure data
Related structure data | 8iskMC 8isiC 8isjC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35693.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_35693_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35693_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Zea mays phytochrome A1 (ZmphyA1-Pr)
Entire | Name: Zea mays phytochrome A1 (ZmphyA1-Pr) |
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Components |
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-Supramolecule #1: Zea mays phytochrome A1 (ZmphyA1-Pr)
Supramolecule | Name: Zea mays phytochrome A1 (ZmphyA1-Pr) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
-Macromolecule #1: Phytochrome
Macromolecule | Name: Phytochrome / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Zea mays (maize) |
Molecular weight | Theoretical: 124.72643 KDa |
Recombinant expression | Organism: Insect cell expression vector pTIE1 (others) |
Sequence | String: 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 |
-Macromolecule #2: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydro...
Macromolecule | 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- ...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 |
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Molecular weight | Theoretical: 586.678 Da |
Chemical component information | ChemComp-O6E: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 229726 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |