[English] 日本語
![](img/lk-miru.gif)
- PDB-8em2: Cryo-EM structure of the human GDH/6PGL endoplasmic bifunctional ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8em2 | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the human GDH/6PGL endoplasmic bifunctional protein | ||||||
![]() | GDH/6PGL endoplasmic bifunctional protein | ||||||
![]() | OXIDOREDUCTASE / H6PD / HYDROLASE | ||||||
Function / homology | ![]() regulation of cortisol biosynthetic process / glucose-6-phosphate dehydrogenase [NAD(P)+] / 6-phosphogluconolactonase / glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / 6-phosphogluconolactonase activity / glucose 1-dehydrogenase [NAD(P)+] / glucose 1-dehydrogenase [NAD(P)+] activity / glucose-6-phosphate dehydrogenase activity / response to alcohol ...regulation of cortisol biosynthetic process / glucose-6-phosphate dehydrogenase [NAD(P)+] / 6-phosphogluconolactonase / glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / 6-phosphogluconolactonase activity / glucose 1-dehydrogenase [NAD(P)+] / glucose 1-dehydrogenase [NAD(P)+] activity / glucose-6-phosphate dehydrogenase activity / response to alcohol / pentose-phosphate shunt, oxidative branch / response to nutrient levels / glucose metabolic process / NADP binding / carbohydrate binding / endoplasmic reticulum lumen / endoplasmic reticulum / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å | ||||||
![]() | Su, C.C. | ||||||
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 | ![]() | 213.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 166 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 44 KB | Display | |
Data in CIF | ![]() | 64.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 23429 ![]() 28232MC ![]() 7uzmC ![]() 8ekwC ![]() 8ekyC ![]() 8emrC ![]() 8emsC ![]() 8emtC ![]() 8eneC ![]() 8eojC ![]() 8eorC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 89001.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: O95479, glucose 1-dehydrogenase [NAD(P)+], glucose-6-phosphate dehydrogenase [NAD(P)+], 6-phosphogluconolactonase #2: Sugar | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: H6PD / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
---|---|
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: This is from a heterogeneous and impure protein sample. |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-
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: 29 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-
Processing
Software | Name: PHENIX / Version: dev_4761: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196757 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||
Refine LS restraints |
|