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Yorodumi- EMDB-27698: Cryo-EM structure of Arabidopsis SPY alternative conformation 2 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27698 | |||||||||
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Title | Cryo-EM structure of Arabidopsis SPY alternative conformation 2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | O-fucosyltransferase / SPY / TRANSFERASE | |||||||||
Function / homology | Function and homology information negative regulation of gibberellic acid mediated signaling pathway / protein N-acetylglucosaminyltransferase activity / peptide-O-fucosyltransferase / gibberellic acid mediated signaling pathway / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / cytokinin-activated signaling pathway / protein O-GlcNAc transferase / protein O-acetylglucosaminyltransferase activity / flower development ...negative regulation of gibberellic acid mediated signaling pathway / protein N-acetylglucosaminyltransferase activity / peptide-O-fucosyltransferase / gibberellic acid mediated signaling pathway / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / cytokinin-activated signaling pathway / protein O-GlcNAc transferase / protein O-acetylglucosaminyltransferase activity / flower development / regulation of reactive oxygen species metabolic process / rhythmic process / cell differentiation / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Kumar S / Zhou Y / Dillard L / Borgnia MJ / Bartesaghi A / Zhou P | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structure of the full length Arabidopsis SPY with complete TPRs Authors: Kumar S / Zhou Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27698.map.gz | 201.1 MB | EMDB map data format | |
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Header (meta data) | emd-27698-v30.xml emd-27698.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27698_fsc.xml | 14.4 KB | Display | FSC data file |
Images | emd_27698.png | 80.4 KB | ||
Masks | emd_27698_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-27698.cif.gz | 5.9 KB | ||
Others | emd_27698_half_map_1.map.gz emd_27698_half_map_2.map.gz | 200.4 MB 200.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27698 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27698 | HTTPS FTP |
-Related structure data
Related structure data | 8dthMC 8dtfC 8dtgC 8dtiC C: citing same article (ref.) M: atomic model generated by this map |
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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_27698.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27698_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27698_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27698_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Apo SPY in alternative conformation 2
Entire | Name: Apo SPY in alternative conformation 2 |
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Components |
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-Supramolecule #1: Apo SPY in alternative conformation 2
Supramolecule | Name: Apo SPY in alternative conformation 2 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
-Macromolecule #1: Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltra...
Macromolecule | Name: Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: protein O-GlcNAc transferase |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 105.278859 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MVGLEDDTER ERSPVVENGF SNGSRSSSSS AGVLSPSRKV TQGNDTLSYA NILRARNKFA DALALYEAML EKDSKNVEAH IGKGICLQT QNKGNLAFDC FSEAIRLDPH NACALTHCGI LHKEEGRLVE AAESYQKALM ADASYKPAAE CLAIVLTDLG T SLKLAGNT ...String: MVGLEDDTER ERSPVVENGF SNGSRSSSSS AGVLSPSRKV TQGNDTLSYA NILRARNKFA DALALYEAML EKDSKNVEAH IGKGICLQT QNKGNLAFDC FSEAIRLDPH NACALTHCGI LHKEEGRLVE AAESYQKALM ADASYKPAAE CLAIVLTDLG T SLKLAGNT QEGIQKYYEA LKIDPHYAPA YYNLGVVYSE MMQYDNALSC YEKAALERPM YAEAYCNMGV IYKNRGDLEM AI TCYERCL AVSPNFEIAK NNMAIALTDL GTKVKLEGDV TQGVAYYKKA LYYNWHYADA MYNLGVAYGE MLKFDMAIVF YEL AFHFNP HCAEACNNLG VLYKDRDNLD KAVECYQMAL SIKPNFAQSL NNLGVVYTVQ GKMDAAASMI EKAILANPTY AEAF NNLGV LYRDAGNITM AIDAYEECLK IDPDSRNAGQ NRLLAMNYIN EGLDDKLFEA HRDWGWRFTR LHPQYTSWDN LKDPE RPIT IGYISPDFFT HSVSYFIEAP LTHHDYTKYK VVVYSAVVKA DAKTYRFRDK VLKKGGVWKD IYGIDEKKIA SMVRED KID ILVELTGHTA NNKLGTMACR PAPVQVTWIG YPNTTGLPTV DYRITDSLAD PPDTKQKQVE ELVRLPDCFL CYTPSPE AG PVCPTPALSN GFVTFGSFNN LAKITPKVLQ VWARILCAVP NSRLVVKCKP FCCDSIRQRF LTTLEQLGLE SKRVDLLP L ILFNHDHMQA YSLMDISLDT FPYAGTTTTC ESLYMGVPCV TMAGSVHAHN VGVSLLTKVG LGHLVAKNED EYVQLSVDL ASDVTALSKL RMSLRDLMAG SPVCNGPSFA VGLESAYRNM WKKYCKGEVP SLRRMEMLQK EVHDDPLISK DLGPSRVSVT GEATPSLKA NGSAPVPSSL PTQSPQLSKR MDSTSGGSEN LYFQGGSHHH HHHHHHHGGW SHPQFEK UniProtKB: Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 289.15 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 54900 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |