4I1O: Legionella pneumophila GAP domain of LepB
Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b bound to GDP and BeF3. Determined by X-ray diffraction at 2.7 Å resolution. Released 16 Jan 2013.
- Method
- X-ray diffraction
- Resolution
- 2.7 Å
- Organisms
- Homo sapiens, Legionella pneumophila subsp. pneumophila
- Chains
- 8
- Atoms
- 14,310
- Mol. weight
- 221.23 kDa
- Ligands
- MG, GDP, BEF
- Released
- 16 Jan 2013
Explore 4I1O in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4I1O contains 101 α-helices and 56 β-strands across 8 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.
Chains A and E: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-14 | 8 | 1 |
| α-helix | 21-30 | 10 | |
| β-strand | 38-39 | 2 | 2 |
| β-strand | 43-52 | 10 | 1 |
| β-strand | 55-64 | 10 | 1 |
| α-helix | 68-70 | 3 | |
| α-helix | 71-74 | 4 | |
| α-helix | 75-77 | 3 | |
| β-strand | 83-89 | 7 | 1 |
| α-helix | 93-97 | 5 | |
| α-helix | 99-109 | 11 | |
| β-strand | 115-121 | 7 | 1 |
| α-helix | 133-141 | 9 | |
| β-strand | 147-149 | 3 | 1 |
| α-helix | 158-178 | 21 | |
Chain B: 17 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 339-351 | 13 | |
| α-helix | 368-387 | 20 | |
| α-helix | 404-406 | 3 | |
| β-strand | 413-414 | 2 | 3 |
| β-strand | 417-418 | 2 | 3 |
| β-strand | 423 | 1 | 4 |
| α-helix | 425-433 | 9 | |
| α-helix | 434 | 1 | |
| β-strand | 435 | 1 | 5 |
| α-helix | 436 | 1 | |
| β-strand | 442-443 | 2 | 5 |
| α-helix | 444 | 1 | |
| α-helix | 446-448 | 3 | |
| α-helix | 449-458 | 10 | |
| α-helix | 463-490 | 28 | |
| α-helix | 493-521 | 29 | |
| β-strand | 538 | 1 | 4 |
| α-helix | 543-547 | 5 | |
| α-helix | 551-561 | 11 | |
| α-helix | 569-575 | 7 | |
| α-helix | 578-580 | 3 | |
| α-helix | 581-589 | 9 | |
| α-helix | 600-614 | 15 | |
Chains C and G: 8 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-15 | 9 | 6 |
| α-helix | 21-30 | 10 | |
| β-strand | 38-39 | 2 | 5 |
| β-strand | 43-52 | 10 | 6 |
| β-strand | 55-64 | 10 | 6 |
| α-helix | 68-70 | 3 | |
| α-helix | 71-74 | 4 | |
| α-helix | 75-77 | 3 | |
| β-strand | 83-89 | 7 | 6 |
| α-helix | 93-97 | 5 | |
| α-helix | 99-109 | 11 | |
| β-strand | 115-121 | 7 | 6 |
| α-helix | 133-141 | 9 | |
| β-strand | 147-149 | 3 | 6 |
| β-strand | 151 | 1 | 7 |
| β-strand | 156 | 1 | 7 |
| α-helix | 158-178 | 21 | |
Chain D: 17 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 330-332 | 3 | |
| α-helix | 339-351 | 13 | |
| α-helix | 367-387 | 21 | |
| α-helix | 404-406 | 3 | |
| β-strand | 413-414 | 2 | 8 |
| β-strand | 417-418 | 2 | 8 |
| β-strand | 423 | 1 | 9 |
| α-helix | 425-433 | 9 | |
| α-helix | 434 | 1 | |
| β-strand | 435 | 1 | 2 |
| α-helix | 436 | 1 | |
| β-strand | 442-443 | 2 | 2 |
| α-helix | 444 | 1 | |
| α-helix | 446-448 | 3 | |
| α-helix | 449-458 | 10 | |
| α-helix | 463-490 | 28 | |
| α-helix | 493-522 | 30 | |
| β-strand | 538 | 1 | 9 |
| α-helix | 543-547 | 5 | |
| α-helix | 551-561 | 11 | |
| α-helix | 569-575 | 7 | |
| α-helix | 581-589 | 9 | |
| α-helix | 600-614 | 15 | |
Chain F: 18 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 330-332 | 3 | |
| α-helix | 339-351 | 13 | |
| α-helix | 367-387 | 21 | |
| α-helix | 404-406 | 3 | |
| β-strand | 413-414 | 2 | 12 |
| β-strand | 417-418 | 2 | 12 |
| β-strand | 423 | 1 | 13 |
| α-helix | 425-433 | 9 | |
| α-helix | 434 | 1 | |
| β-strand | 435 | 1 | 11 |
| α-helix | 436 | 1 | |
| β-strand | 442-443 | 2 | 11 |
| α-helix | 444 | 1 | |
| α-helix | 446-448 | 3 | |
| α-helix | 449-458 | 10 | |
| α-helix | 463-490 | 28 | |
| α-helix | 493-521 | 29 | |
| β-strand | 538 | 1 | 13 |
| α-helix | 543-547 | 5 | |
| α-helix | 551-561 | 11 | |
| α-helix | 569-576 | 8 | |
| α-helix | 578-580 | 3 | |
| α-helix | 581-589 | 9 | |
| α-helix | 600-615 | 16 | |
Chain H: 17 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 330-332 | 3 | |
| α-helix | 339-351 | 13 | |
| α-helix | 368-387 | 20 | |
| α-helix | 404-406 | 3 | |
| β-strand | 413-414 | 2 | 17 |
| β-strand | 417-418 | 2 | 17 |
| β-strand | 423 | 1 | 18 |
| α-helix | 425-433 | 9 | |
| α-helix | 434 | 1 | |
| β-strand | 435 | 1 | 15 |
| α-helix | 436 | 1 | |
| β-strand | 442-443 | 2 | 15 |
| α-helix | 444 | 1 | |
| α-helix | 446-448 | 3 | |
| α-helix | 449-458 | 10 | |
| α-helix | 463-490 | 28 | |
| α-helix | 493-522 | 30 | |
| β-strand | 538 | 1 | 18 |
| α-helix | 543-547 | 5 | |
| α-helix | 551-561 | 11 | |
| α-helix | 569-575 | 7 | |
| α-helix | 581-589 | 9 | |
| α-helix | 600-614 | 15 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ras-related protein Rab-1B | A, C, E, G | protein | 181 | Homo sapiens | Q9H0U4 (AlphaFold model) |
| LepB | B, D, F, H | protein | 302 | Legionella pneumophila subsp. pneumophila | Q5ZSM7 |
Sequence of entity 1 (A, C, E, G), FASTA
>4I1O_1 Ras-related protein Rab-1B (chains A, C, E, G)
GHMPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKL
QIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLV
GNKSDLTTKKVVDNTTAKEFADSLGIPFLETSAKNATNVEQAFMTMAAEIKKRMGLEVLF
Q
Sequence of entity 2 (B, D, F, H), FASTA
>4I1O_2 LepB (chains B, D, F, H)
EELYQSILELKPLTLLMTSSTSFSETINQWADILKTTDMEKFSFDSNPINLLELVKQFNL
YVDELAITCEANNVWAKERIDSTPNLFALYDNSGGEAIHGHAFVPYYKESIVLRRLFTVD
PNTFNLSRFAAFEGPCQLYCAAHADSAWVKIQTLLTLGNGIINTLKIIKQAQAFGIDEAV
TENLKALKEQFIAFQLAEADIKESLKAPSFAEPLPNKESEFFYPIDEKALAKMNGYQLAT
ICLEELNSPKPSPLIERILSNKKFWKRINSAFESGVFKGRTDDPAGKIAKIREWHQLLQI
SG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 4 |
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 4 |
| BEF | Beryllium trifluoride ion | Be F3 | 4 |
Water and common crystallization additives (PEG) are not listed.
Primary citation
Mechanism of Rab1b deactivation by the Legionella pneumophila GAP LepB. Mihai Gazdag, E., Streller, A., Haneburger, I. et al. EMBO Rep (2013) 14:199-205. DOI 10.1038/embor.2012.211 · PubMed
Other PDB entries of the same protein (UniProt Q9H0U4 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3NKV 1.7 Å, Crystal structure of Rab1b covalently modified with AMP at Y77
- 3JZA 1.8 Å, Crystal structure of human Rab1b in complex with the GEF domain of DrrA/SidM from…
- 8ALK 2.15 Å, Structure of the Legionella phosphocholine hydrolase Lem3 in complex with its substrate…
- 5SZH 2.3 Å, Structure of human Rab1b in complex with the bMERB domain of Mical-cL
- 5O74 2.5 Å, Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from…
- 5SZK 2.8 Å, Structure of human N-terminally engineered Rab1b in complex with the bMERB domain of…
- 6SKU 3.2 Å, Legionella effector AnkX in complex with human Rab1b
- 4HLQ 3.3 Å, Crystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of…
Browse structure collections
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