+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27700 | |||||||||
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Title | Overall map of Arabidopsis SPY in complex with GDP-fucose | |||||||||
Map data | NU refinement Overall Map | |||||||||
Sample |
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Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Kumar S / Zhou Y / Lucas D / 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_27700.map.gz | 117.9 MB | EMDB map data format | |
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Header (meta data) | emd-27700-v30.xml emd-27700.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27700_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_27700.png | 68.6 KB | ||
Masks | emd_27700_msk_1.map | 125 MB | Mask map | |
Others | emd_27700_half_map_1.map.gz emd_27700_half_map_2.map.gz | 115.7 MB 115.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27700 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27700 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27700.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | NU refinement Overall Map | ||||||||||||||||||||
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
-Mask #1
File | emd_27700_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_27700_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_27700_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SPY GDP-fucose complex
Entire | Name: SPY GDP-fucose complex |
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Components |
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-Supramolecule #1: SPY GDP-fucose complex
Supramolecule | Name: SPY GDP-fucose complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
-Macromolecule #1: SPY GDP-fucose complex
Macromolecule | Name: SPY GDP-fucose complex / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MVGLEDDTER ERSPVVENGF SNGSRSSSSS AGVLSPSRKV TQGNDTLSYA NILRARNKFA DALALYEAML EKDSKNVEAH IGKGICLQTQ NKGNLAFDCF SEAIRLDPHN ACALTHCGIL HKEEGRLVEA AESYQKALMA DASYKPAAEC LAIVLTDLGT SLKLAGNTQE ...String: MVGLEDDTER ERSPVVENGF SNGSRSSSSS AGVLSPSRKV TQGNDTLSYA NILRARNKFA DALALYEAML EKDSKNVEAH IGKGICLQTQ NKGNLAFDCF SEAIRLDPHN ACALTHCGIL HKEEGRLVEA AESYQKALMA DASYKPAAEC LAIVLTDLGT SLKLAGNTQE GIQKYYEALK IDPHYAPAYY NLGVVYSEMM QYDNALSCYE KAALERPMYA EAYCNMGVIY KNRGDLEMAI TCYERCLAVS PNFEIAKNNM AIALTDLGTK VKLEGDVTQG VAYYKKALYY NWHYADAMYN LGVAYGEMLK FDMAIVFYEL AFHFNPHCAE ACNNLGVLYK DRDNLDKAVE CYQMALSIKP NFAQSLNNLG VVYTVQGKMD AAASMIEKAI LANPTYAEAF NNLGVLYRDA GNITMAIDAY EECLKIDPDS RNAGQNRLLA MNYINEGLDD KLFEAHRDWG WRFTRLHPQY TSWDNLKDPE RPITIGYISP DFFTHSVSYF IEAPLTHHDY TKYKVVVYSA VVKADAKTYR FRDKVLKKGG VWKDIYGIDE KKIASMVRED KIDILVELTG HTANNKLGTM ACRPAPVQVT WIGYPNTTGL PTVDYRITDS LADPPDTKQK QVEELVRLPD CFLCYTPSPE AGPVCPTPAL SNGFVTFGSF NNLAKITPKV LQVWARILCA VPNSRLVVKC KPFCCDSIRQ RFLTTLEQLG LESKRVDLLP LILFNHDHMQ AYSLMDISLD TFPYAGTTTT CESLYMGVPC VTMAGSVHAH NVGVSLLTKV GLGHLVAKNE DEYVQLSVDL ASDVTALSKL RMSLRDLMAG SPVCNGPSFA VGLESAYRNM WKKYCKGEVP SLRRMEMLQK EVHDDPLISK DLGPSRVSVT GEATPSLKAN GSAPVPSSLP TQSPQLSKRM DSTSGGSENL YFQGGSHHHH HHHHHHGGWS HPQFEK |
-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 / Support film - Film thickness: 40.0 nm / Pretreatment - Type: PLASMA CLEANING | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 289.15 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 52.4 e/Å2 |
Electron beam | Acceleration voltage: 300 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: 0.8 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |