6ZSJ: 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 2.0 Å resolution. Released 2 Sept 2020.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,179
Mol. weight: 79.2 kDa
Ligands: MG, GNP
Released: 2 Sept 2020

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

Secondary structure: helices and β-sheets

6ZSJ contains 23 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: 9 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	99-107	9
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	158-173	16

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	158-173	16

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	1075-1104	30
α-helix	1110-1160	51
α-helix	1169-1202	34

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	1075-1105	31
α-helix	1109-1160	52
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

>6ZSJ_1 Ras-related protein Rab-8A (chains A, B)
GHMAKTYDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIK
LQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMI
LGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKK

Sequence of entity 2 (C, D), FASTA

>6ZSJ_2 EH domain-binding protein 1 (chains C, D)
GHMDEVLNKGFKDTSQYVVGELAALENEQKQIDTRAALVEKRLRYLMDTGRNTEEEEAMM
QEWAMLVNKKNALIRRMNQLSLLEKEHDLERRYELLNRELRAMLAIEDWQKTEAQKRREQ
LLLDELVALVNKRDALVRDLDAQEKQAEEEDEHLER

Ligands and cofactors

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

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
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
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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