[English] 日本語
![](img/lk-miru.gif)
- PDB-8r4c: LRR domain of Roco protein from C. tepidum bound to the activatin... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8r4c | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | LRR domain of Roco protein from C. tepidum bound to the activating Nanobody NbRoco2 | ||||||||||||
![]() |
| ||||||||||||
![]() | ![]() ![]() ![]() ![]() | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Galicia, C. / Versees, W. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Structural insights into the GTP-driven monomerization and activation of a bacterial LRRK2 homolog using allosteric nanobodies. Authors: Christian Galicia / Giambattista Guaitoli / Marcus Fislage / Christian Johannes Gloeckner / Wim Versées / ![]() ![]() Abstract: Roco proteins entered the limelight after mutations in human LRRK2 were identified as a major cause of familial Parkinson's disease. LRRK2 is a large and complex protein combining a GTPase and ...Roco proteins entered the limelight after mutations in human LRRK2 were identified as a major cause of familial Parkinson's disease. LRRK2 is a large and complex protein combining a GTPase and protein kinase activity, and disease mutations increase the kinase activity, while presumably decreasing the GTPase activity. Although a cross-communication between both catalytic activities has been suggested, the underlying mechanisms and the regulatory role of the GTPase domain remain unknown. Several structures of LRRK2 have been reported, but structures of Roco proteins in their activated GTP-bound state are lacking. Here, we use single-particle cryo-electron microscopy to solve the structure of a bacterial Roco protein (CtRoco) in its GTP-bound state, aided by two conformation-specific nanobodies: Nb and Nb. This structure presents CtRoco in an active monomeric state, featuring a very large GTP-induced conformational change using the LRR-Roc linker as a hinge. Furthermore, this structure shows how Nb and Nb collaborate to activate CtRoco in an allosteric way. Altogether, our data provide important new insights into the activation mechanism of Roco proteins, with relevance to LRRK2 regulation, and suggest new routes for the allosteric modulation of their GTPase activity. #1: ![]() Title: Structural insights in the GTP-driven monomerization and activation of a bacterial LRRK2 homologue using allosteric nanobodies Authors: Galicia, C. / Guaitoli, G. / Fislage, M. / Gloeckner, C.J. / Versees, W. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 118.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 79.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 18885MC ![]() 8r4bC ![]() 8r4dC C: citing same article ( M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Antibody | Mass: 14180.744 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 124313.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: LRR domain of CtRoco / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
-
Sample preparation
Component | Name: CtRoco in the active GTP state bound to the two activating Nanobodies NbRoco1 and NbRoco2 Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Value: 0.15 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Cryogen name: ETHANE / Humidity: 90 % |
-
Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
---|---|
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Image recording | Electron dose: 63 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
EM software | Name: cryoSPARC / Category: 3D reconstruction![]() | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160925 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1
| ||||||||||||||||||||||||
Refine LS restraints |
|