4IRU: LepB

Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3. Determined by X-ray diffraction at 3.2 Å resolution. Released 10 Jul 2013.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Legionella pneumophila, Homo sapiens
Chains: 6
Atoms: 11,410
Mol. weight: 168.61 kDa
Ligands: AF3, GDP, MG
Released: 10 Jul 2013

Explore 4IRU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4IRU contains 68 α-helices and 50 β-strands across 6 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: 17 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	326	1
β-strand	327-329	3	1
α-helix	339-352	14
β-strand	358-360	3	1
α-helix	367-387	21
α-helix	390-393	4
α-helix	404-406	3
β-strand	413-414	2	2
β-strand	417-418	2	2
β-strand	423	1	3
α-helix	425-433	9
β-strand	436	1	4
β-strand	441	1	4
β-strand	442-443	2	5
α-helix	446-448	3
α-helix	449-457	9
α-helix	463-489	27
α-helix	493-520	28
α-helix	522-524	3
β-strand	538	1	3
α-helix	543-547	5
α-helix	551-561	11
α-helix	567-568	2
α-helix	569-576	8
α-helix	578-589	12
α-helix	600-617	18

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	6
α-helix	24-33	10
β-strand	41-42	2	5
α-helix	43-44	2
β-strand	46-55	10	6
β-strand	58-67	10	6
α-helix	71-73	3
α-helix	74-79	6
β-strand	86-92	7	6
α-helix	96-112	17
β-strand	118	1	6
β-strand	121-124	4	6
α-helix	136-145	10
β-strand	150-152	3	6
α-helix	161-174	14

Chain C: 17 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	327-329	3	7
α-helix	339-351	13
β-strand	358-360	3	7
α-helix	367-387	21
α-helix	390-394	5
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
β-strand	436	1	10
β-strand	441	1	10
β-strand	442-443	2	11
α-helix	444	1
α-helix	446-448	3
α-helix	449-457	9
α-helix	463-489	27
α-helix	493-520	28
α-helix	523-524	2
α-helix	528-531	4
β-strand	538	1	9
α-helix	543-547	5
α-helix	551-561	11
α-helix	569-576	8
α-helix	578-589	12
α-helix	600-619	20

Chain D: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	12
α-helix	24-33	10
β-strand	41-42	2	11
α-helix	43-44	2
β-strand	46-55	10	12
β-strand	58-67	10	12
α-helix	71-73	3
α-helix	74-79	6
β-strand	86-92	7	12
α-helix	96-112	17
β-strand	118-124	7	12
α-helix	129-131	3
α-helix	136-145	10
β-strand	150-152	3	12
α-helix	161-175	15

Chain E: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	328-329	2	13
α-helix	339-351	13
β-strand	359-360	2	13
α-helix	367-378	12
α-helix	404-406	3
β-strand	414	1	14
β-strand	417	1	14
β-strand	423	1	15
α-helix	425-432	8
β-strand	435	1	16
β-strand	442-443	2	16
α-helix	449-453	5
α-helix	463-470	8
α-helix	475-490	16
α-helix	493-514	22
α-helix	523-524	2
β-strand	538	1	15
α-helix	545-548	4
α-helix	551-561	11
α-helix	569-573	5
α-helix	578-588	11
α-helix	600-615	16

Chain F: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	17
α-helix	24-32	9
β-strand	41-42	2	16
β-strand	50-52	3	17
β-strand	60-66	7	17
α-helix	75-78	4
β-strand	87-92	6	17
α-helix	96-99	4
β-strand	119-124	6	17
α-helix	141-144	4
β-strand	150-151	2	17
β-strand	154	1	18
β-strand	159	1	18
α-helix	173-175	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
LepB	A, C, E	protein	299	Legionella pneumophila	Q5ZSM7
Ras-related protein Rab-1A	B, D, F	protein	184	Homo sapiens	P62820 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>4IRU_1 LepB (chains A, C, E)
SLKPLTLLMTSSTSFSETINQWADILKTTDMEKFSFDSNPINLLELVKQFNLYVDELAIT
CEANNVWAKERIDSTPNLFALYDNSGGEAIHGHAFVPYYKESIVLRRLFTVDPNTFNLSR
FAAFEGPCQLYCKEHKDSAWVKIQTLLTLGNGIINTLKIIKQAQAFGIDEAVTENLKALK
EQFIAFQLAEADIKESLKAPSFAEPLPNKESEFFYPIDEKALAKMNGYQLATICLEELNS
PKPSPLIERILSNKKFWKRINSAFESGVFKGRTDDPAGKIAKIREWHQLLQISGKKTAG

Sequence of entity 2 (B, D, F), FASTA

>4IRU_2 Ras-related protein Rab-1A (chains B, D, F)
MGHHHHHHGSMNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTI
ELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYA
SENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIK
KRMG

Ligands and cofactors

ID	Name	Formula	Copies
AF3	Aluminum fluoride	Al F3	3
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	3
MG	Magnesium ion	Mg	3

Water and common crystallization additives (K, GOL, ACT) are not listed.

Primary citation

The Legionella pneumophila GTPase Activating Protein LepB Accelerates Rab1 Deactivation by a Non-canonical Hydrolytic Mechanism. Mishra, A.K., Del Campo, C.M., Collins, R.E. et al. J Biol Chem (2013) 288:24000-24011. DOI 10.1074/jbc.M113.470625 · PubMed

Other PDB entries of the same protein (UniProt Q5ZSM7), best resolution first:

4I1O 2.7 Å, Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b…
4I1M 2.8 Å, Crystal structure of the Legionella pneumophila GAP domain of LepB

Browse structure collections

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