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- PDB-7pm4: Cryo-EM structures of human fucosidase FucA1 reveal insight into ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pm4 | |||||||||||||||
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Title | Cryo-EM structures of human fucosidase FucA1 reveal insight into substate recognition and catalysis. | |||||||||||||||
![]() | Tissue alpha-L-fucosidase | |||||||||||||||
![]() | HYDROLASE / Fucosidase | |||||||||||||||
Function / homology | ![]() alpha-L-fucosidase / glycolipid catabolic process / glycosaminoglycan catabolic process / Reactions specific to the complex N-glycan synthesis pathway / alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosomal lumen / azurophil granule lumen / lysosome ...alpha-L-fucosidase / glycolipid catabolic process / glycosaminoglycan catabolic process / Reactions specific to the complex N-glycan synthesis pathway / alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosomal lumen / azurophil granule lumen / lysosome / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.49 Å | |||||||||||||||
![]() | Armstrong, Z. / Meek, R.W. / Wu, L. / Blaza, J.N. / Davies, G.J. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of human fucosidase FucA1 reveal insight into substrate recognition and catalysis. Authors: Zachary Armstrong / Richard W Meek / Liang Wu / James N Blaza / Gideon J Davies / ![]() Abstract: Enzymatic hydrolysis of α-L-fucose from fucosylated glycoconjugates is consequential in bacterial infections and the neurodegenerative lysosomal storage disorder fucosidosis. Understanding human α- ...Enzymatic hydrolysis of α-L-fucose from fucosylated glycoconjugates is consequential in bacterial infections and the neurodegenerative lysosomal storage disorder fucosidosis. Understanding human α-L-fucosidase catalysis, in an effort toward drug design, has been hindered by the absence of three-dimensional structural data for any animal fucosidase. Here, we have used cryoelectron microscopy (cryo-EM) to determine the structure of human lysosomal α-L-fucosidase (FucA1) in both an unliganded state and in complex with the inhibitor deoxyfuconojirimycin. These structures, determined at 2.49 Å resolution, reveal the homotetrameric structure of FucA1, the architecture of the catalytic center, and the location of both natural population variations and disease-causing mutations. Furthermore, this work has conclusively identified the hitherto contentious identity of the catalytic acid/base as aspartate-276, representing a shift from both the canonical glutamate acid/base residue and a previously proposed glutamate residue. These findings have furthered our understanding of how FucA1 functions in both health and disease. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 304.6 KB | Display | ![]() |
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PDB format | ![]() | 254.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 13520MC ![]() 7plsC 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: 50525.625 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-DFU / ( #4: Water | ChemComp-HOH / | 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: FucA1 homotetramer in complex with deoxyfuconojirimycin Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 225 kDa/nm / Experimental value: YES | ||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 4.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / 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: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K / Details: blot for 2 seconds before plunging |
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Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | ||||||||||||||||
3D reconstruction | Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98815 / Symmetry type: POINT |