5LPN: Human Rab10

Structure of human Rab10 in complex with the bMERB domain of Mical-1. Determined by X-ray diffraction at 2.8 Å resolution. Released 24 Aug 2016.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,747
Mol. weight: 59.35 kDa
Ligands: GNP, MG
Released: 24 Aug 2016

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

Secondary structure: helices and β-sheets

5LPN contains 21 α-helices and 15 β-strands across 3 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	8-16	9	1
α-helix	22-31	10
β-strand	44-53	10	1
β-strand	56-65	10	1
α-helix	66	1
α-helix	69-71	3
α-helix	72-76	5
α-helix	79-81	3
β-strand	84-90	7	1
α-helix	94-98	5
α-helix	100-110	11
β-strand	116-122	7	1
α-helix	134-144	11
β-strand	147-151	5	1
β-strand	152	1	2
β-strand	157	1	2
α-helix	159-172	14

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	919-959	41
α-helix	963-969	7
α-helix	970-974	5
α-helix	975-1013	39
α-helix	1027-1059	33

Chain C: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	3
α-helix	22-31	10
β-strand	44-51	8	3
α-helix	53-55	3
β-strand	58-65	8	3
α-helix	69-72	4
α-helix	74-79	6
β-strand	84-90	7	3
α-helix	100-110	11
β-strand	118-122	5	3
α-helix	134-144	11
β-strand	152	1	4
β-strand	157	1	4
α-helix	159-171	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-10	A, C	protein	177	Homo sapiens	P61026 (AlphaFold model)
Protein-methionine sulfoxide oxidase MICAL1	B	protein	153	Homo sapiens	Q8TDZ2 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5LPN_1 Ras-related protein Rab-10 (chains A, C)
GHMAKKTYDLLFKLLLIGDSGVGKTCVLFRFSDDAFNTTFISTIGIDFKIKTVELQGKKI
KLQIWDTAGQERFHTITTSYYRGAMGIMLVYDITNGKSFENISKWLRNIDEHANEDVERM
LLGNKCDMDDKRVVPKGKGEQIAREHGIRFFETSAKANINIEKAFLTLAEDILRKTP

Sequence of entity 2 (B), FASTA

>5LPN_2 Protein-methionine sulfoxide oxidase MICAL1 (chains B)
GHMKEEEMKRFCKAQTIQRRLNEIEAALRELEAEGVKLELALRRQSSSPEQQKKLWVGQL
LQLVDKKNSLVAEEAELMITVQELNLEEKQWQLDQELRGYMNREENLKTAADRQAEDQVL
RKLVDLVNQRDALIRFQEERRLSELALGTGAQG

Ligands and cofactors

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

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 P61026 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9G0C 1.8 Å, Structure of human Mical1 bMERB_V978A_V985A domain:Rab10 complex.
9G0D 2.05 Å, Structure of human Mical1 bMERB_V978A domain:Rab10 complex.
5SZJ 2.66 Å, Structure of human Rab10 in complex with the bMERB domain of Mical-cL

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