+
Open data
-
Basic information
Entry | Database: PDB / ID: 8emr | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of human liver glucosidase II | ||||||
![]() |
| ||||||
![]() | HYDROLASE / glucosidase II / GANAB / glycosyl hydrolase 31 family | ||||||
Function / homology | ![]() mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / Calnexin/calreticulin cycle / glucosidase II complex / alpha-glucosidase activity / Maturation of spike protein / N-glycan processing / Advanced glycosylation endproduct receptor signaling / liver development / N-glycan trimming in the ER and Calnexin/Calreticulin cycle ...mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / Calnexin/calreticulin cycle / glucosidase II complex / alpha-glucosidase activity / Maturation of spike protein / N-glycan processing / Advanced glycosylation endproduct receptor signaling / liver development / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / phosphoprotein binding / protein kinase C binding / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / carbohydrate binding / Maturation of spike protein / transmembrane transporter binding / carbohydrate metabolic process / intracellular signal transduction / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / calcium ion binding / Golgi apparatus / endoplasmic reticulum / RNA binding / extracellular exosome / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å | ||||||
![]() | Su, C. / Lyu, M. / Zhang, Z. / Yu, E.W. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: High-resolution structural-omics of human liver enzymes. Authors: Chih-Chia Su / Meinan Lyu / Zhemin Zhang / Masaru Miyagi / Wei Huang / Derek J Taylor / Edward W Yu / ![]() Abstract: We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined ...We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined high-resolution structural information for ten unique human liver enzymes involved in diverse cellular processes. Notably, we determined the structure of the endoplasmic bifunctional protein H6PD, where the N- and C-terminal domains independently possess glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase enzymatic activity, respectively. We also obtained the structure of heterodimeric human GANAB, an ER glycoprotein quality-control machinery that contains a catalytic α subunit and a noncatalytic β subunit. In addition, we observed a decameric peroxidase, PRDX4, which directly contacts a disulfide isomerase-related protein, ERp46. Structural data suggest that several glycosylations, bound endogenous compounds, and ions associate with these human liver enzymes. These results highlight the importance of cryo-EM in facilitating the elucidation of human organ proteomics at the atomic level. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 211.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 159.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 41.9 KB | Display | |
Data in CIF | ![]() | 61.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 28262MC ![]() 7uzmC ![]() 8ekwC ![]() 8ekyC ![]() 8em2C ![]() 8emsC ![]() 8emtC ![]() 8eneC ![]() 8eojC ![]() 8eorC ![]() 23434 M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 106997.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q14697, mannosyl-oligosaccharide alpha-1,3-glucosidase | ||
---|---|---|---|
#2: Protein | Mass: 59485.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||
#4: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: glucosidase II / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL |
---|---|
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 41.25 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-
Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129601 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|