[English] 日本語
![](img/lk-miru.gif)
- PDB-7q5r: Protein community member pyruvate dehydrogenase complex E2 core f... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7q5r | ||||||
---|---|---|---|---|---|---|---|
Title | Protein community member pyruvate dehydrogenase complex E2 core from C. thermophilum | ||||||
![]() | Acetyltransferase component of pyruvate dehydrogenase complex | ||||||
![]() | TRANSFERASE / Dihydrolipoyl / transacetylase / E2 / Pyruvate | ||||||
Function / homology | ![]() dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase complex / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.84 Å | ||||||
![]() | Chojnowski, G. / Skalidis, I. / Kyrilis, F.L. / Tueting, C. / Hamdi, F. / Kastritis, P.L. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Cryo-EM and artificial intelligence visualize endogenous protein community members. Authors: Ioannis Skalidis / Fotis L Kyrilis / Christian Tüting / Farzad Hamdi / Grzegorz Chojnowski / Panagiotis L Kastritis / ![]() Abstract: Cellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and ...Cellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and thioesters of coenzyme-A synthesis. Metabolons are highly heterogeneous due to their function, making their analysis particularly challenging. Here, we simultaneously characterize metabolon-embedded architectures of a 60S pre-ribosome, fatty acid synthase, and pyruvate/oxoglutarate dehydrogenase complex E2 cores de novo. Cryo-electron microscopy (cryo-EM) 3D reconstructions are resolved at 3.84-4.52 Å resolution by collecting <3,000 micrographs of a single cellular fraction. After combining cryo-EM with artificial intelligence-based atomic modeling and de novo sequence identification methods, at this resolution range, polypeptide hydrogen bonding patterns are discernible. Residing molecular components resemble their purified counterparts from other eukaryotes but also exhibit substantial conformational variation with potential functional implications. Our results propose an integrated tool, boosted by machine learning, that opens doors for structural systems biology spearheaded by cryo-EM characterization of native cell extracts. | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 2.2 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 13845MC ![]() 7q5qC ![]() 7q5sC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | |
EM raw data | ![]() Data size: 1.1 TB Data #1: Unaligned fractions saved by Falcon 3 EC camera [micrographs - multiframe]) |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
|