+
Open data
-
Basic information
Entry | Database: PDB / ID: 6r8u | ||||||
---|---|---|---|---|---|---|---|
Title | Escherichia coli AGPase in complex with AMP. | ||||||
![]() | Glucose-1-phosphate adenylyltransferase | ||||||
![]() | TRANSFERASE / ADP-glucose pyrophosphorilase Complex with AMP inhibitor | ||||||
Function / homology | ![]() glucose-1-phosphate adenylyltransferase complex / glucose-1-phosphate adenylyltransferase / glucose-1-phosphate adenylyltransferase activity / glycogen biosynthetic process / AMP binding / protein homotetramerization / magnesium ion binding / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
![]() | Cifuente, J.O. / Comino, N. / D'Angelo, C. / Marina, A. / Gil-Carton, D. / Albesa-Jove, D. / Guerin, M.E. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: The allosteric control mechanism of bacterial glycogen biosynthesis disclosed by cryoEM Authors: Cifuente, J.O. / Comino, N. / D'Angelo, C. / Marina, A. / Gil-Carton, D. / Albesa-Jove, D. / Guerin, M.E. | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 549 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 460.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 51.8 KB | Display | |
Data in CIF | ![]() | 78.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4761MC ![]() 4754C ![]() 6r8bC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 48758.590 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Complex with AMP / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A6V1, glucose-1-phosphate adenylyltransferase #2: Chemical | ChemComp-AMP / |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: ADP.glucose pyrophosphorylase in complex with the inhibitor AMP Type: COMPLEX / Details: Homotetrameric enzyme / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.194 MDa / Experimental value: NO | ||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||
Buffer component |
| ||||||||||||||||
Specimen | Conc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Sample with single particles and some linear chains of particles | ||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 283 K |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS / Details: Titan Krios I - Ebic - Diamond Light Source |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 |
-
Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| |||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94769 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5L6V Accession code: 5L6V / Source name: PDB / Type: experimental model |