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- PDB-7ufu: Cryo-EM Structure of Bl_Man38A nucleophile mutant in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ufu | |||||||||
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Title | Cryo-EM Structure of Bl_Man38A nucleophile mutant in complex with mannose at 2.7 A | |||||||||
![]() | Alpha-mannosidase | |||||||||
![]() | HYDROLASE / n-glycan / probiotic / a-mannosidase / gh38 | |||||||||
Function / homology | ![]() alpha-mannosidase activity / mannose metabolic process / oligosaccharide catabolic process / fungal-type vacuole membrane / carbohydrate binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
![]() | Santos, C.R. / Cordeiro, R.L. / Domingues, M.N. / Borges, A.C. / de Farias, M.A. / Van Heel, M. / Murakami, M.T. / Portugal, R.V. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM Structure of Bl_Man38A nucleophile mutant in complex with mannose at 2.7 A Authors: Santos, C.R. / Cordeiro, R.L. / Domingues, M.N. / Borges, A.C. / de Farias, M.A. / Van Heel, M. / Murakami, M.T. / Portugal, R.V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 714.6 KB | Display | ![]() |
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PDB format | ![]() | 580 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 26481MC 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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Components
#1: Protein | Mass: 117943.125 Da / Num. of mol.: 4 / Mutation: D410A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Sugar | ChemComp-MAN / 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: Tetramer of nucleophile mutant version of Bl1_Man38A in complex with mannose Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.471 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 Details: 150 mM sodium chloride, 20 mM sodium phosphate, pH 7.5 |
Specimen | Conc.: 2.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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 / Cs: 0.01 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 1.5 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k 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 | |||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16231 / Symmetry type: POINT | |||||||||||||||||||||||||||
Refine LS restraints |
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