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Yorodumi- EMDB-13499: Cryo-EM structures of human fucosidase FucA1 reveal insight into ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13499 | |||||||||||||||
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Title | Cryo-EM structures of human fucosidase FucA1 reveal insight into substate recognition and catalysis. | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.49 Å | |||||||||||||||
Authors | Armstrong Z / Meek RW / Wu L / Blaza JN / Davies GJ | |||||||||||||||
Funding support | United Kingdom, 4 items
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Citation | Journal: Structure / Year: 2022 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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13499.map.gz | 8.9 MB | EMDB map data format | |
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Header (meta data) | emd-13499-v30.xml emd-13499.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_13499.png | 158.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13499 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13499 | HTTPS FTP |
-Validation report
Summary document | emd_13499_validation.pdf.gz | 330.4 KB | Display | EMDB validaton report |
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Full document | emd_13499_full_validation.pdf.gz | 330 KB | Display | |
Data in XML | emd_13499_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_13499_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13499 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13499 | HTTPS FTP |
-Related structure data
Related structure data | 7plsMC 7pm4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13499.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: 0.934 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : FucA1 homotetramer
Entire | Name: FucA1 homotetramer |
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Components |
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-Supramolecule #1: FucA1 homotetramer
Supramolecule | Name: FucA1 homotetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Molecular weight | Experimental: 225 kDa/nm |
-Macromolecule #1: Tissue alpha-L-fucosidase
Macromolecule | Name: Tissue alpha-L-fucosidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: alpha-L-fucosidase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50.525625 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: GQPPRRYTPD WPSLDSRPLP AWFDEAKFGV FIHWGVFSVP AWGSEWFWWH WQGEGRPQYQ RFMRDNYPPG FSYADFGPQF TARFFHPEE WADLFQAAGA KYVVLTTKHH EGFTNWPSPV SWNWNSKDVG PHRDLVGELG TALRKRNIRY GLYHSLLEWF H PLYLLDKK ...String: GQPPRRYTPD WPSLDSRPLP AWFDEAKFGV FIHWGVFSVP AWGSEWFWWH WQGEGRPQYQ RFMRDNYPPG FSYADFGPQF TARFFHPEE WADLFQAAGA KYVVLTTKHH EGFTNWPSPV SWNWNSKDVG PHRDLVGELG TALRKRNIRY GLYHSLLEWF H PLYLLDKK NGFKTQHFVS AKTMPELYDL VNSYKPDLIW SDGEWECPDT YWNSTNFLSW LYNDSPVKDE VVVNDRWGQN CS CHHGGYY NCEDKFKPQS LPDHKWEMCT SIDKFSWGYR RDMALSDVTE ESEIISELVQ TVSLGGNYLL NIGPTKDGLI VPI FQERLL AVGKWLSING EAIYASKPWR VQWEKNTTSV WYTSKGSAVY AIFLHWPENG VLNLESPITT STTKITMLGI QGDL KWSTD PDKGLFISLP QLPPSAVPAE FAWTIKLTGV K |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 52 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2 seconds before plunging. |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
-Image processing
Final reconstruction | Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 171847 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |