5O74: Human Rab1b covalently
Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP. Determined by X-ray diffraction at 2.5 Å resolution. Released 11 Oct 2017.
- Method
- X-ray diffraction
- Resolution
- 2.5 Å
- Organisms
- Legionella pneumophila, Homo sapiens
- Chains
- 12
- Atoms
- 17,004
- Mol. weight
- 258.3 kDa
- Ligands
- GDP
- Released
- 11 Oct 2017
Explore 5O74 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5O74 contains 107 α-helices and 66 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 12 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 343-361 | 19 | |
| α-helix | 365-382 | 18 | |
| α-helix | 386-389 | 4 | |
| α-helix | 390-393 | 4 | |
| α-helix | 400-419 | 20 | |
| α-helix | 428-447 | 20 | |
| α-helix | 452-454 | 3 | |
| α-helix | 458-460 | 3 | |
| α-helix | 461-463 | 3 | |
| α-helix | 464-478 | 15 | |
| β-strand | 484-485 | 2 | 1 |
| β-strand | 488-489 | 2 | 1 |
| α-helix | 490-506 | 17 | |
| α-helix | 512-520 | 9 | |
| β-strand | 528 | 1 | 2 |
Chain B: 9 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-14 | 8 | 3 |
| α-helix | 21-24 | 4 | |
| α-helix | 25-27 | 3 | |
| β-strand | 29 | 1 | 3 |
| α-helix | 30-32 | 3 | |
| α-helix | 36-41 | 6 | |
| β-strand | 45-52 | 8 | 3 |
| β-strand | 55-62 | 8 | 3 |
| α-helix | 67-69 | 3 | |
| α-helix | 75-77 | 3 | |
| β-strand | 83-89 | 7 | 3 |
| α-helix | 93-109 | 17 | |
| β-strand | 115-121 | 7 | 3 |
| α-helix | 133-142 | 10 | |
| β-strand | 147-150 | 4 | 3 |
| β-strand | 151 | 1 | 4 |
| β-strand | 156 | 1 | 4 |
| α-helix | 158-172 | 15 | |
Chain C: 10 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 342-361 | 20 | |
| α-helix | 365-382 | 18 | |
| α-helix | 386-389 | 4 | |
| α-helix | 390-393 | 4 | |
| α-helix | 400-419 | 20 | |
| α-helix | 428-447 | 20 | |
| α-helix | 452-454 | 3 | |
| α-helix | 464-478 | 15 | |
| β-strand | 484-485 | 2 | 5 |
| β-strand | 488-489 | 2 | 5 |
| α-helix | 490-506 | 17 | |
| α-helix | 512-520 | 9 | |
Chain D: 7 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-14 | 8 | 6 |
| α-helix | 21-24 | 4 | |
| β-strand | 29 | 1 | 6 |
| α-helix | 30-32 | 3 | |
| α-helix | 36-41 | 6 | |
| β-strand | 45-52 | 8 | 6 |
| β-strand | 55-62 | 8 | 6 |
| α-helix | 67-69 | 3 | |
| β-strand | 83-89 | 7 | 6 |
| α-helix | 93-108 | 16 | |
| β-strand | 115-121 | 7 | 6 |
| α-helix | 133-143 | 11 | |
| β-strand | 147-150 | 4 | 6 |
| β-strand | 151 | 1 | 7 |
| β-strand | 156 | 1 | 7 |
| α-helix | 158-172 | 15 | |
Chain E: 10 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 343-361 | 19 | |
| α-helix | 365-382 | 18 | |
| α-helix | 386-389 | 4 | |
| α-helix | 390-393 | 4 | |
| α-helix | 400-419 | 20 | |
| α-helix | 428-447 | 20 | |
| α-helix | 452-454 | 3 | |
| α-helix | 464-478 | 15 | |
| β-strand | 484-485 | 2 | 8 |
| β-strand | 488-489 | 2 | 8 |
| α-helix | 490-506 | 17 | |
| α-helix | 512-520 | 9 | |
Chain F: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-14 | 8 | 9 |
| α-helix | 21-28 | 8 | |
| α-helix | 37-41 | 5 | |
| β-strand | 45-52 | 8 | 9 |
| β-strand | 55-62 | 8 | 9 |
| α-helix | 67-69 | 3 | |
| α-helix | 75-77 | 3 | |
| β-strand | 83-89 | 7 | 9 |
| α-helix | 93-109 | 17 | |
| β-strand | 115-121 | 7 | 9 |
| α-helix | 133-143 | 11 | |
| β-strand | 147-150 | 4 | 9 |
| β-strand | 151 | 1 | 10 |
| β-strand | 156 | 1 | 10 |
| α-helix | 158-172 | 15 | |
Chain G: 10 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 342-361 | 20 | |
| α-helix | 365-381 | 17 | |
| α-helix | 386-389 | 4 | |
| α-helix | 390-393 | 4 | |
| α-helix | 400-419 | 20 | |
| α-helix | 428-447 | 20 | |
| α-helix | 452-454 | 3 | |
| α-helix | 464-478 | 15 | |
| β-strand | 484-485 | 2 | 11 |
| β-strand | 488-489 | 2 | 11 |
| α-helix | 490-506 | 17 | |
| α-helix | 512-520 | 9 | |
| β-strand | 528 | 1 | 3 |
Chain H: 8 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-14 | 8 | 2 |
| α-helix | 21-24 | 4 | |
| α-helix | 25-27 | 3 | |
| β-strand | 29 | 1 | 2 |
| α-helix | 36-41 | 6 | |
| β-strand | 45-52 | 8 | 2 |
| β-strand | 55-62 | 8 | 2 |
| α-helix | 67-69 | 3 | |
| α-helix | 75-78 | 4 | |
| β-strand | 83-89 | 7 | 2 |
| α-helix | 93-109 | 17 | |
| β-strand | 115-121 | 7 | 2 |
| α-helix | 133-142 | 10 | |
| β-strand | 147-150 | 4 | 2 |
| β-strand | 151 | 1 | 12 |
| β-strand | 156 | 1 | 12 |
| α-helix | 158-172 | 15 | |
3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Multifunctional virulence effector protein DrrA | A, C, E, G, I, K | protein | 197 | Legionella pneumophila | Q29ST3 (AlphaFold model) |
| Ras-related protein Rab-1B | B, D, F, H, J, L | protein | 180 | Homo sapiens | Q9H0U4 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G, I, K), FASTA
>5O74_1 Multifunctional virulence effector protein DrrA (chains A, C, E, G, I, K)
GHMVTRIENLENAKKLWDNANSMLEKGNISGYLKAANELHKFMKEKNLKEDDLRPELSDK
TISPKGYAILQSLWGAASDYSRAAATLTESTVEPGLVSAVNKMSAFFMDCKLSPNERATP
DPDFKVGKSKILVGIMQFIKDVADPTSKIWMHNTKALMNHKIAAIQKLERSNNVNCETLE
SVLSSKGENLSEYLSYK
Sequence of entity 2 (B, D, F, H, J, L), FASTA
>5O74_2 Ras-related protein Rab-1B (chains B, D, F, H, J, L)
MAPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQ
IWDTAGQERFRTITSSYYXGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVG
NKSDLTTKKVVDNTTAKEFADSLGIPFLETSAKNATNVEQAFMTMAAEIKKRMGHHHHHH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 6 |
Primary citation
Proximity-Triggered Covalent Stabilization of Low-Affinity Protein Complexes In Vitro and In Vivo. Cigler, M., Muller, T.G., Horn-Ghetko, D. et al. Angew Chem Int Ed Engl (2017) 56:15737-15741. DOI 10.1002/anie.201706927 · PubMed
Other PDB entries of the same protein (UniProt Q29ST3 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3NKU 2.1 Å, Crystal structure of the N-terminal domain of DrrA/SidM from Legionella pneumophila
- 6YX5 2.14 Å, Structure of DrrA from Legionella pneumophilia in complex with human Rab8a
Browse structure collections
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