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Yorodumi- EMDB-27699: Cryo-EM structure of Arabidopsis SPY in complex with GDP-fucose -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27699 | |||||||||
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Title | Cryo-EM structure of Arabidopsis SPY in complex with GDP-fucose | |||||||||
Map data | ||||||||||
Sample |
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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: 3.8 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_27699.map.gz | 117 MB | EMDB map data format | |
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Header (meta data) | emd-27699-v30.xml emd-27699.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27699_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_27699.png | 79 KB | ||
Others | emd_27699_additional_1.map.gz emd_27699_additional_2.map.gz emd_27699_additional_3.map.gz | 117.9 MB 118.2 MB 118 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27699 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27699 | HTTPS FTP |
-Related structure data
Related structure data | 8dtiMC 8dtfC 8dtgC 8dthC 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_27699.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: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Overall lower resolution map
File | emd_27699_additional_1.map | ||||||||||||
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Annotation | Overall lower resolution map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused component map (monomer B)
File | emd_27699_additional_2.map | ||||||||||||
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Annotation | Focused component map (monomer B) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused component map (monomer A)
File | emd_27699_additional_3.map | ||||||||||||
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Annotation | Focused component map (monomer A) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SPY in complex with GDP-fucose
Entire | Name: SPY in complex with GDP-fucose |
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Components |
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-Supramolecule #1: SPY in complex with GDP-fucose
Supramolecule | Name: SPY in complex with GDP-fucose / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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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: Spodoptera frugiperda (fall armyworm) |
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 |
-Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE / type: ligand / ID: 2 / Number of copies: 2 / Formula: GFB |
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Molecular weight | Theoretical: 589.342 Da |
Chemical component information | ChemComp-GFB: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |