3SFV: GDP-bound Rab1a S25N mutant

Crystal structure of the GDP-bound Rab1a S25N mutant in complex with the coiled-coil domain of LidA from Legionella pneumophila. Determined by X-ray diffraction at 1.73 Å resolution. Released 18 Apr 2012.

Method: X-ray diffraction
Resolution: 1.73 Å
Organisms: Homo sapiens, Legionella pneumophila
Chains: 2
Atoms: 4,656
Mol. weight: 61.11 kDa
Ligands: GDP
Released: 18 Apr 2012

Explore 3SFV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3SFV contains 25 α-helices and 19 β-strands across 2 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	10-17	8	1
α-helix	24-33	10
β-strand	47-55	9	1
β-strand	58-66	9	1
α-helix	67-68	2
α-helix	71-73	3
α-helix	77-80	4
β-strand	86-92	7	1
α-helix	96-100	5
α-helix	102-112	11
β-strand	118-124	7	1
α-helix	129-131	3
α-helix	136-146	11
β-strand	150-152	3	1
α-helix	161-173	13

Chain B: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	226-248	23
α-helix	250-256	7
α-helix	257-261	5
α-helix	262-285	24
α-helix	290-318	29
β-strand	322-324	3	2
β-strand	330	1	2
α-helix	334-336	3
β-strand	339-341	3	2
β-strand	345-350	6	3
β-strand	353-358	6	3
α-helix	362-365	4
α-helix	369-413	45
α-helix	418-448	31
β-strand	452-455	4	4
β-strand	461-462	2	4
α-helix	465-467	3
β-strand	470-473	4	4
β-strand	476-481	6	5
β-strand	484-489	6	5
β-strand	492-497	6	6
β-strand	500-505	6	6
α-helix	510-513	4
α-helix	517-528	12
α-helix	529-532	4
β-strand	536	1	4
α-helix	538-562	25
α-helix	563-565	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-1A	A	protein	181	Homo sapiens	P62820 (AlphaFold model)
LidA protein, substrate of the Dot/Icm system	B	protein	344	Legionella pneumophila	Q5ZWZ3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3SFV_1 Ras-related protein Rab-1A (chains A)
GPLGSMSSMNPEYDYLFKLLLIGDSGVGKNCLLLRFADDTYTESYISTIGVDFKIRTIEL
DGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASE
NVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKR
M

Sequence of entity 2 (B), FASTA

>3SFV_2 LidA protein, substrate of the Dot/Icm system (chains B)
KKLDKLERQGKDLEDKYKTYEENLEGFEKLLTDSEELSLSEINEKMKAFSKDSEKLTQLM
EKHKGDEKTVQSLQREHHDIKAKLANLQVLHDAHTGKKSYVNEKGNPVSSLKDAHLAINK
DQEVVEHKGQFYLLQKGQWDAIKNDPAALEKAQKDYSQSKHDLATIKMEALIHKLSLEME
KQLETINDLIMSTDPKENEEATKLLHKHNGLNLKLANLQDMLAVHRKEKSFFNEKGEKVT
SLNDAHYVIGKDQQLFNLGGKFYPIHKEQKILEKDGKFYLLKQGEDWESIKDSPEKQKKA
EHDFHKLQYETPMTVKKLVHHNKGLETTIHKERIEELEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Primary citation

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. et al. PLoS Pathog (2012) 8:e1002528-e1002528. DOI 10.1371/journal.ppat.1002528 · PubMed

Other PDB entries of the same protein (UniProt P62820 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2WWX 1.5 Å, Crystal structure of the SidM/DrrA(GEF/GDF domain)-Rab1(GTPase domain) complex
7EQ2 1.55 Å, Crystal structure of GDP-bound Rab1a-T75D
3TKL 2.18 Å, Crystal structure of the GTP-bound Rab1a in complex with the coiled-coil domain of LidA…
2FOL 2.63 Å, Crystal structure of human RAB1A in complex with GDP
9MHF 2.73 Å, Cryo-EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L)
4JVS 2.78 Å, Crystal structure of LepB GAP domain from Legionella drancourtii in complex with…
4FMC 2.8 Å, EspG-Rab1 complex
3L0I 2.85 Å, Complex structure of SidM/DrrA with the wild type Rab1
4FMD 3.05 Å, EspG-Rab1 complex structure at 3.05 A
4FMB 3.2 Å, VirA-Rab1 complex structure
4IRU 3.2 Å, Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and…
9MHG 3.2 Å, Cryo EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L), VPS34 kinase…

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