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Open data
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Basic information
Entry | Database: PDB / ID: 8dti | ||||||
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Title | Cryo-EM structure of Arabidopsis SPY in complex with GDP-fucose | ||||||
![]() | Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY | ||||||
![]() | TRANSFERASE / O-fucosyltransferase / SPY | ||||||
Function / homology | ![]() 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 / protein O-GlcNAc transferase / cytokinin-activated signaling pathway / 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 / protein O-GlcNAc transferase / cytokinin-activated signaling pathway / protein O-acetylglucosaminyltransferase activity / flower development / regulation of reactive oxygen species metabolic process / rhythmic process / cell differentiation / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
![]() | Kumar, S. / Zhou, Y. / Dillard, L. / Borgnia, M.J. / Bartesaghi, A. / Zhou, P. | ||||||
Funding support | ![]()
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![]() | ![]() 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229.8 KB | Display | ![]() |
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PDB format | ![]() | 174.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 978 KB | Display | ![]() |
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Full document | ![]() | 986.8 KB | Display | |
Data in XML | ![]() | 42.7 KB | Display | |
Data in CIF | ![]() | 65.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27699MC ![]() 8dtfC ![]() 8dtgC ![]() 8dthC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 105278.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q96301, protein O-GlcNAc transferase, peptide-O-fucosyltransferase #2: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: SPY in complex with GDP-fucose / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 52.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182947 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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