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- Structure Factors (CIF - gz)
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- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
3SFV | pdb_00003sfv
Crystal structure of the GDP-bound Rab1a S25N mutant in complex with the coiled-coil domain of LidA from Legionella pneumophila
- PDB DOI: https://doi.org/10.2210/pdb3SFV/pdb
- Classification: protein transport/protein binding
- Organism(s): Homo sapiens, Legionella pneumophila str. Corby
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2011-06-14 Released: 2012-04-18
- Deposition Author(s): Yin, K., Lu, D., Zhu, D., Zhang, H., Li, B., Xu, S., Gu, L.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.73 Å
- R-Value Free: 0.228 (Depositor), 0.220 (DCC)
- R-Value Work: 0.192 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.193 (Depositor)
Starting Model: experimental
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Structural Insights into a Unique Legionella pneumophila Effector LidA Recognizing Both GDP and GTP Bound Rab1 in Their Active State
Cheng, W., Yin, K., Lu, D., Li, B., Zhu, D., Chen, Y., Zhang, H., Xu, S., Chai, J., Gu, L.(2012) PLoS Pathog 8: e1002528-e1002528
- PubMed: 22416225 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.1371/journal.ppat.1002528
- Primary Citation Related Structures:
3SFV, 3TKL - PubMed Abstract:
The intracellular pathogen Legionella pneumophila hijacks the endoplasmic reticulum (ER)-derived vesicles to create an organelle designated Legionella-containing vacuole (LCV) required for bacterial replication. Maturation of the LCV involved acquisition of Rab1, which is mediated by the bacterial effector protein SidM/DrrA. SidM/DrrA is a bifunctional enzyme having the activity of both Rab1-specific GDP dissociation inhibitor (GDI) displacement factor (GDF) and guanine nucleotide exchange factor (GEF). LidA, another Rab1-interacting bacterial effector protein, was reported to promote SidM/DrrA-mediated recruitment of Rab1 to the LCV as well. Here we report the crystal structures of LidA complexes with GDP- and GTP-bound Rab1 respectively. Structural comparison revealed that GDP-Rab1 bound by LidA exhibits an active and nearly identical conformation with that of GTP-Rab1, suggesting that LidA can disrupt the switch function of Rab1 and render it persistently active. As with GTP, LidA maintains GDP-Rab1 in the active conformation through interaction with its two conserved switch regions. Consistent with the structural observations, biochemical assays showed that LidA binds to GDP- and GTP-Rab1 equally well with an affinity approximately 7.5 nM. We propose that the tight interaction with Rab1 allows LidA to facilitate SidM/DrrA-catalyzed release of Rab1 from GDIs. Taken together, our results support a unique mechanism by which a bacterial effector protein regulates Rab1 recycling.
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China.
Organizational Affiliation:
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (GDP)
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (GDP)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 2-mer - A1B1
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 61.11 kDa
- Atom Count: 4,656
- Modeled Residue Count: 521
- Deposited Residue Count: 525
- Unique protein chains: 2
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ras-related protein Rab-1A | 181 | Homo sapiens | Mutation(s): 1 Gene Names: RAB1A EC: 3.6.5.2 | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P62820 (Homo sapiens) Explore P62820 Go to UniProtKB: P62820 | |||||
PHAROS: P62820 GTEx: ENSG00000138069 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P62820 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| LidA protein, substrate of the Dot/Icm system | 344 | Legionella pneumophila str. Corby | Mutation(s): 0 Gene Names: lidA | 👁 Image | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GDP Query on GDP Download Ideal Coordinates CCD File | C [auth A] | GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N | 👁 Image | ||
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.73 Å
- R-Value Free: 0.228 (Depositor), 0.220 (DCC)
- R-Value Work: 0.192 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.193 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 154.314 | α = 90 |
| b = 54.673 | β = 90 |
| c = 61.699 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| PHASER | phasing |
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Deposition Data
Revision History (Full details and data files)
- Version 1.0: 2012-04-18
Type: Initial release - Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
