6YX5: DrrA from Legionella pneumophilia

Structure of DrrA from Legionella pneumophilia in complex with human Rab8a. Determined by X-ray diffraction at 2.14 Å resolution. Released 23 Dec 2020.

Method: X-ray diffraction
Resolution: 2.14 Å
Organisms: Homo sapiens, Legionella pneumophila
Chains: 2
Atoms: 4,353
Mol. weight: 60.8 kDa
Ligands: LJN, GLC, GNP, MG
Released: 23 Dec 2020

Explore 6YX5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YX5 contains 28 α-helices and 16 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	43-52	10	1
β-strand	55-64	10	1
α-helix	68-70	3
α-helix	71-75	5
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	133-142	10
β-strand	146-149	4	1
β-strand	151	1	2
β-strand	156	1	2
α-helix	158-174	17

Chain B: 20 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	16	1
β-strand	17	1	3
α-helix	18	1
β-strand	29	1	3
α-helix	31-53	23
α-helix	61-83	23
α-helix	87-89	3
β-strand	93-96	4	4
α-helix	98-101	4
β-strand	113-116	4	4
α-helix	121-144	24
β-strand	160-161	2	4
α-helix	163-171	9
α-helix	178-186	9
β-strand	189-190	2	4
α-helix	196-207	12
α-helix	209-211	3
α-helix	217-222	6
α-helix	223-227	5
α-helix	229-232	4
β-strand	237-239	3	5
α-helix	241-245	5
α-helix	246-258	13
α-helix	267-269	3
α-helix	271-280	10
α-helix	286-310	25
β-strand	316-318	3	5
α-helix	319-348	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-8A	A	protein	174	Homo sapiens	P61006 (AlphaFold model)
Multifunctional virulence effector protein DrrA	B	protein	340	Legionella pneumophila	Q29ST3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6YX5_1 Ras-related protein Rab-8A (chains A)
SHMDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIW
DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNK
CDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKK

Sequence of entity 2 (B), FASTA

>6YX5_2 Multifunctional virulence effector protein DrrA (chains B)
GHMFGSLYSDERDKPLLSPTAQKKFEEYQNKLANLSKIIRENEGNEVSPWQEWENGLRQI
YKEMIYDAFDALGVEMPKDMEVHFAGSLAKAQATEYSDLDAFVIVKNDEDIKKVKPVFDA
LNNLCQRIFTASNQIYPDPIGINPSRLIGTPDDLFGMLKDGMVADVEATAMSILTSKPVL
PRYECGEELRDKIKQEPSFSNMVSAKKFYNKAIKDFTAPKEGAEVVSVKTHIMRPIDFML
MGLREEFNLYSEDGAHLSAPGTIRLLREKNLLPEEQIARIESVYNQAMSKRFELHAEHKK
EHDEMPYSDAKAMLDEVAKIRELGVQRVTRIENLENAKKL

Ligands and cofactors

ID	Name	Formula	Copies
LJN	[(2~{R},3~{S},4~{R},5~{R})-5-[4-(acetamidomethyl)-1,2,3-triazol-1-yl]-3,4-bis(o…	C10 H17 N4 O8 P	1
GLC	alpha-D-glucopyranose	C6 H12 O6	3
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Rab1-AMPylation by Legionella DrrA is allosterically activated by Rab1. Du, J., Wrisberg, M.V., Gulen, B. et al. Nat Commun (2021) 12:460-460. DOI 10.1038/s41467-020-20702-2 · 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.
7BWT 2.3 Å, SopD-Rab8 complex structure

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