5SZI: Human Rab8a

Structure of human Rab8a in complex with the bMERB domain of Mical-cL. Determined by X-ray diffraction at 2.85 Å resolution. Released 24 Aug 2016.

Method: X-ray diffraction
Resolution: 2.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,461
Mol. weight: 42.91 kDa
Ligands: MG, GNP
Released: 24 Aug 2016

Explore 5SZI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5SZI contains 10 α-helices and 8 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: 6 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	68-76	9
β-strand	83-89	7	1
α-helix	93-97	5
α-helix	99-109	11
β-strand	117-121	5	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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	538-571	34
α-helix	583-632	50
α-helix	635-637	3
α-helix	640-678	39

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-8A	A	protein	209	Homo sapiens	P61006 (AlphaFold model)
MICAL C-terminal-like protein	B	protein	153	Homo sapiens	O94851 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5SZI_1 Ras-related protein Rab-8A (chains A)
GHMAKTYDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIK
LQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMI
LGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKKLE
GNSPQGSNQGVKITPDQQKRSSFFRCVLL

Sequence of entity 2 (B), FASTA

>5SZI_2 MICAL C-terminal-like protein (chains B)
GHMKQEELKRLYKAQAIQRQLEEVEERQRASEIQGVRLEKALRGEADSGTQDEAQLLQEW
FKLVLEKNKLMRYESELLIMAQELELEDHQSRLEQKLREKMLKEESQKDEKDLNEEQEVF
TELMQVIEQRDKLVDSLEEQRIREKAEDQHFES

Ligands and cofactors

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

Primary citation

bMERB domains are bivalent Rab8 family effectors evolved by gene duplication. Rai, A., Oprisko, A., Campos, J. et al. Elife (2016) 5. DOI 10.7554/eLife.18675 · 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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