3TNF: LidA from Legionella

LidA from Legionella in complex with active Rab8a. Determined by X-ray diffraction at 2.5 Å resolution. Released 2 Nov 2011.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Chains: 2
Atoms: 4,590
Mol. weight: 65.67 kDa
Ligands: MG, GNP
Released: 2 Nov 2011

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

Secondary structure: helices and β-sheets

3TNF contains 23 α-helices and 21 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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	1
α-helix	21-30	10
β-strand	44-52	9	1
β-strand	55-63	9	1
α-helix	68-70	3
α-helix	74-77	4
β-strand	83-89	7	1
α-helix	93-97	5
α-helix	99-109	11
β-strand	115-121	7	1
α-helix	126-128	3
α-helix	133-143	11
β-strand	146-149	4	1
β-strand	151	1	2
β-strand	156	1	2
α-helix	158-174	17

Chain B: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	203-213	11
α-helix	221-225	5
α-helix	228-248	21
α-helix	251-254	4
α-helix	257-261	5
α-helix	262-283	22
α-helix	290-317	28
β-strand	322-324	3	3
β-strand	330-331	2	3
α-helix	334-336	3
β-strand	339-341	3	3
β-strand	345-348	4	4
β-strand	355-358	4	4
α-helix	369-414	46
α-helix	418-448	31
β-strand	452-455	4	5
β-strand	461-462	2	5
α-helix	465-467	3
β-strand	470-473	4	5
β-strand	476-480	5	6
β-strand	485-489	5	6
β-strand	492-497	6	7
β-strand	500-505	6	7
α-helix	510-513	4
α-helix	517-530	14
β-strand	536	1	5
α-helix	538-569	32
α-helix	571-578	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-8A	A	protein	174	Homo sapiens	P61006 (AlphaFold model)
LidA	B	protein	384	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Q5ZWZ3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3TNF_1 Ras-related protein Rab-8A (chains A)
GHMDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIW
DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNK
CDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKK

Sequence of entity 2 (B), FASTA

>3TNF_2 LidA (chains B)
GMLDEYEQAIKRAQENIKKGEELEKKLDKLERQGKDLEDKYKTYEENLEGFEKLLTDSEE
LSLSEINEKMEAFSKDSEKLTQLMEKHKGDEKTVQSLQREHHDIKAKLANLQVLHDAHTG
KKSYVNEKGNPVSSLKDAHLAINKDQEVVEHEGQFYLLQKGQWDAIKNNPAALEKAQKDY
SQSKHDLATIKMEALIHKLSLEMEKQLETINNLIMSTDPKENEEATKLLHKHNGLNLKLA
NLQDMLAVHRKEKSFFNEKGEEVTSLNDAHYVIGKDQQLFNLGGKFYPIHKEQKILEKDG
KFYLLKQGEDWESIKDSPEKQKKAEHDFHKLQYETPMTVKKLVHHNKGLETTIHKERVEE
TKQQLEDNGKEKIEIANNISKLQS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1

Water and common crystallization additives (MPD) are not listed.

Primary citation

Protein LidA from Legionella is a Rab GTPase supereffector. Schoebel, S., Cichy, A.L., Goody, R.S. et al. Proc Natl Acad Sci U S A (2011) 108:17945-17950. DOI 10.1073/pnas.1113133108 · PubMed

Other PDB entries of the same protein (UniProt P61006 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LHW 1.55 Å, Crystal structure of Rab8 in its active GppNHp-bound form
6SQ2 1.68 Å, Structure of a phosphomimetic switch 2 variant of Rab8a in complex with the phospho-Rab…
6WHE 1.73 Å, Structure of phosphomimetic Rab8a GTPase (T72E) in the GTP-bound state
6RIR 1.77 Å, Crystal structure of phosphorylated Rab8a in complex with the Rab-binding domain of RILPL2
9M0O 1.83 Å, Crystal structure of OPTN 138-170 in complex with GTP-bound RAB8A1-176 (Q67L)
7LWB 1.9 Å, Crystal Structure of phospho-Rab8a with the RH2 domain (117-165) of RILPL2
6ZSI 1.91 Å, The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members.
9IKQ 1.93 Å, Crystal structure of OPTN LZD in complex with GTP-bound Rab8a(Q67L)
4LHV 1.95 Å, Crystal structure of Rab8 in its inactive GDP-bound form
3QBT 2.0 Å, Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp
6ZSJ 2.0 Å, The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members.
6YX5 2.14 Å, Structure of DrrA from Legionella pneumophilia in complex with human Rab8a

Browse structure collections

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