6SQ2: Phosphomimetic switch 2 variant of Rab8a

Structure of a phosphomimetic switch 2 variant of Rab8a in complex with the phospho-Rab binding domain of RILPL2. Determined by X-ray diffraction at 1.68 Å resolution. Released 30 Sept 2020.

Method: X-ray diffraction
Resolution: 1.68 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,974
Mol. weight: 53.84 kDa
Ligands: MG, GTP
Released: 30 Sept 2020

Explore 6SQ2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SQ2 contains 18 α-helices and 18 β-strands across 4 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	71-74	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	133-143	11
β-strand	146-149	4	1
β-strand	151	1	2
β-strand	156	1	2
α-helix	158-175	18

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	3
α-helix	21-30	10
β-strand	43-52	10	3
β-strand	55-64	10	3
α-helix	68-70	3
α-helix	71-75	5
β-strand	83-89	7	3
α-helix	93-97	5
α-helix	99-109	11
β-strand	115-121	7	3
α-helix	126-128	3
α-helix	133-143	11
β-strand	146-149	4	3
β-strand	151	1	4
β-strand	156	1	4
α-helix	158-174	17

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	133	1	5
α-helix	135-157	23

Chain E: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	133	1	5
α-helix	135-156	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-8A	A, B	protein	184	Homo sapiens	P61006 (AlphaFold model)
RILP-like protein 2	D, E	protein	43	Homo sapiens	Q969X0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6SQ2_1 Ras-related protein Rab-8A (chains A, B)
GSHMAKTYDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRI
KLQIWDTAGLERFREITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKM
ILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKKL
EGNS

Sequence of entity 2 (D, E), FASTA

>6SQ2_2 RILP-like protein 2 (chains D, E)
HHHHHHNRPRFTLQELRDVLQERNKLKSQLLVVQEELQCYKSG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

Primary citation

Structure of a phosphomimetic switch 2 variant of Rab8a in complex with the phospho-Rab binding domain of RILPL2. Khan, A.R., Waschbusch, D. To be published.

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
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
7BWT 2.3 Å, SopD-Rab8 complex structure

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