+
Open data
-
Basic information
Entry | Database: PDB / ID: 7f5u | ||||||
---|---|---|---|---|---|---|---|
Title | Drosophila P5CS filament with glutamate and ATPgammaS | ||||||
![]() | Delta-1-pyrroline-5-carboxylate synthase | ||||||
![]() | TRANSFERASE / filament / ALDH18A1 / Delta-1-pyrroline-5-carboxylate synthase / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | ![]() Glutamate and glutamine metabolism / Mitochondrial protein degradation / glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / L-proline biosynthetic process / proline biosynthetic process / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
![]() | Liu, J.L. / Zhong, J. / Guo, C.J. / Zhou, X. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural basis of dynamic P5CS filaments. Authors: Jiale Zhong / Chen-Jun Guo / Xian Zhou / Chia-Chun Chang / Boqi Yin / Tianyi Zhang / Huan-Huan Hu / Guang-Ming Lu / Ji-Long Liu / ![]() Abstract: The bifunctional enzyme Δ-pyrroline-5-carboxylate synthase (P5CS) is vital to the synthesis of proline and ornithine, playing an essential role in human health and agriculture. Pathogenic mutations ...The bifunctional enzyme Δ-pyrroline-5-carboxylate synthase (P5CS) is vital to the synthesis of proline and ornithine, playing an essential role in human health and agriculture. Pathogenic mutations in the P5CS gene (ALDH18A1) lead to neurocutaneous syndrome and skin relaxation connective tissue disease in humans, and P5CS deficiency seriously damages the ability to resist adversity in plants. We have recently found that P5CS forms cytoophidia in vivo and filaments in vitro. However, it is difficult to appreciate the function of P5CS filamentation without precise structures. Using cryo-electron microscopy, here we solve the structures of full-length P5CS in three states at resolution from 3.1 to 4.3 Å. We observe distinct ligand-binding states and conformational changes for the GK and GPR domains, respectively. Divergent helical filaments are assembled by P5CS tetramers and stabilized by multiple interfaces. Point mutations disturbing those interfaces prevent P5CS filamentation and greatly reduce the enzymatic activity. Our findings reveal that filamentation is crucial for the coordination between the GK and GPR domains, providing a structural basis for the catalytic function of P5CS filaments. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 449.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 372.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 31467MC ![]() 7f5tC ![]() 7f5vC ![]() 7f5xC ![]() 7wx3C ![]() 7wx4C ![]() 7wxfC ![]() 7wxgC ![]() 7wxhC ![]() 7wxiC 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: 84198.227 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: Q9VNW6, glutamate 5-kinase, glutamate-5-semialdehyde dehydrogenase |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Drosophila Delta-1-pyrroline-5-carboxylate synthase bound with ATP-gamma-S and Glutamate Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | 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: DARK FIELD |
Image recording | Electron dose: 72 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 292974 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|