6ZSI: Ras-related protein Rab-8A

The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. Determined by X-ray diffraction at 1.91 Å resolution. Released 2 Sept 2020.

Method: X-ray diffraction
Resolution: 1.91 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,111
Mol. weight: 79.45 kDa
Ligands: GNP, MG
Released: 2 Sept 2020

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

Secondary structure: helices and β-sheets

6ZSI contains 24 α-helices and 16 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	71-75	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	133-143	11
β-strand	146-149	4	1
β-strand	151	1	2
β-strand	156	1	2
α-helix	158-170	13

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	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	158-173	16

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	1076-1101	26
α-helix	1110-1160	51
α-helix	1164-1166	3
α-helix	1169-1198	30

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	1076-1104	29
α-helix	1111-1160	50
α-helix	1164-1166	3
α-helix	1169-1203	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-8A	A, B	protein	178	Homo sapiens	P61006 (AlphaFold model)
EH domain-binding protein 1	C, D	protein	156	Homo sapiens	Q8NDI1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6ZSI_1 Ras-related protein Rab-8A (chains A, B)
GHMAKTYDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIK
LQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMI
LGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKK

Sequence of entity 2 (C, D), FASTA

>6ZSI_2 EH domain-binding protein 1 (chains C, D)
GHMDEVLNKGFKDTSQYVVGELAALENEQKQIDTRAALVEKRLRYLMDTGRNTEEEEAMA
QEWFMLVNKKNALIRRMNQLSLLEKEHDLERRYELLNRELRAMLAIEDWQKTEAQKRREQ
LLLDELVALVNKRDALVRDLDAQEKQAEEEDEHLER

Ligands and cofactors

ID	Name	Formula	Copies
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2
MG	Magnesium ion	Mg	2

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

Primary citation

The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. Rai, A., Bleimling, N., Vetter, I.R. et al. Nat Commun (2020) 11:4187-4187. DOI 10.1038/s41467-020-17792-3 · 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
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

Browse structure collections

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