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Open data
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Basic information
Entry | Database: PDB / ID: 6lz1 | ||||||||||||
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Title | Structure of S.pombe alpha-mannosidase Ams1 | ||||||||||||
![]() | Ams1 | ||||||||||||
![]() | HYDROLASE / glycoside hydrolase | ||||||||||||
Function / homology | ![]() mannosyl-oligosaccharide 1,6-alpha-mannosidase activity / mannosyl-oligosaccharide 1,3-alpha-mannosidase activity / Lysosomal oligosaccharide catabolism / alpha-mannosidase / fungal-type vacuole lumen / alpha-mannosidase activity / mannose metabolic process / oligosaccharide catabolic process / fungal-type vacuole membrane / carbohydrate binding ...mannosyl-oligosaccharide 1,6-alpha-mannosidase activity / mannosyl-oligosaccharide 1,3-alpha-mannosidase activity / Lysosomal oligosaccharide catabolism / alpha-mannosidase / fungal-type vacuole lumen / alpha-mannosidase activity / mannose metabolic process / oligosaccharide catabolic process / fungal-type vacuole membrane / carbohydrate binding / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
![]() | Zhang, J. / Ye, K. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of fission yeast tetrameric α-mannosidase Ams1. Authors: Jianxiu Zhang / Ying-Ying Wang / Li-Lin Du / Keqiong Ye / ![]() Abstract: Fungal α-mannosidase Ams1 and its mammalian homolog MAN2C1 hydrolyze terminal α-linked mannoses in free oligosaccharides released from misfolded glycoproteins or lipid-linked oligosaccharide donors. ...Fungal α-mannosidase Ams1 and its mammalian homolog MAN2C1 hydrolyze terminal α-linked mannoses in free oligosaccharides released from misfolded glycoproteins or lipid-linked oligosaccharide donors. Ams1 is transported by selective autophagy into vacuoles. Here, we determine the tetrameric structure of Ams1 from the fission yeast Schizosaccharomyces pombe at 3.2 Å resolution by cryo-electron microscopy. Distinct from a low resolution structure of S. cerevisiae Ams1, S. pombe Ams1 has a prominent N-terminal tail that mediates tetramerization and an extra β-sheet domain. Ams1 shares a conserved active site with other enzymes in glycoside hydrolase family 38, to which Ams1 belongs, but contains extra N-terminal domains involved in tetramerization. The atomic structure of Ams1 reported here will aid understanding of its enzymatic activity and transport mechanism. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 752.2 KB | Display | ![]() |
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PDB format | ![]() | 614.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 114 KB | Display | |
Data in CIF | ![]() | 171.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30021MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 129201.672 Da / Num. of mol.: 4 / Fragment: Znic ion Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ams1, mns2, SPAC513.05 / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / 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: Ams1 tetramer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.48 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / 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: 277 K / Details: blot for 5 seconds before plunging |
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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: 1000 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 8.4 sec. / Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 597 |
EM imaging optics | Energyfilter name: GIF Tridiem 4K / Energyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE |
Image scans | Movie frames/image: 32 |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75460 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6LZ1 Accession code: 6LZ1 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.48 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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