8JC5: PLEKHM1 RUN domain

Crystal structure of PLEKHM1 RUN domain in complex with GTP-bound Arl8b(Q75L). Determined by X-ray diffraction at 2.01 Å resolution. Released 27 Mar 2024.

Method: X-ray diffraction
Resolution: 2.01 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,083
Mol. weight: 83.69 kDa
Ligands: GTP, MG
Released: 27 Mar 2024

Explore 8JC5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JC5 contains 48 α-helices and 28 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: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	20-27	8	1
α-helix	33-42	10
α-helix	51-52	2
β-strand	55-62	8	1
β-strand	65-72	8	1
α-helix	76-78	3
α-helix	81-86	6
β-strand	91-97	7	1
α-helix	101-103	3
α-helix	104-115	12
α-helix	118-120	3
β-strand	125-130	6	1
α-helix	140-146	7
α-helix	149-151	3
β-strand	157-161	5	1
β-strand	163	1	2
β-strand	168	1	2
α-helix	170-178	9

Chain B: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	19-27	9	3
α-helix	33-42	10
α-helix	50-53	4
β-strand	55-62	8	3
β-strand	65-72	8	3
α-helix	76-78	3
α-helix	79-86	8
β-strand	91-97	7	3
α-helix	101-103	3
α-helix	104-115	12
α-helix	118-120	3
β-strand	125-130	6	3
α-helix	140-146	7
α-helix	149-151	3
β-strand	157-161	5	3
β-strand	163	1	4
β-strand	168	1	4
α-helix	170-178	9

Chain C: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	14-32	19
β-strand	39-40	2	5
α-helix	45-59	15
β-strand	62	1	6
α-helix	64-67	4
β-strand	70-71	2	7
β-strand	80-81	2	7
α-helix	90-95	6
α-helix	99-106	8
α-helix	114-127	14
α-helix	131-140	10
α-helix	142-148	7
β-strand	149	1	6
α-helix	154-156	3
α-helix	158-169	12
α-helix	170-173	4
β-strand	175-176	2	5
α-helix	183-186	4
α-helix	190-195	6
α-helix	201-203	3

Chain D: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	14-32	19
β-strand	40-41	2	8
α-helix	45-59	15
β-strand	62	1	9
α-helix	64-66	3
β-strand	67-68	2	10
β-strand	86-87	2	10
α-helix	90-94	5
α-helix	99-106	8
α-helix	114-128	15
α-helix	131-140	10
α-helix	142-148	7
β-strand	149	1	9
α-helix	154-156	3
α-helix	158-169	12
α-helix	170-173	4
β-strand	176-177	2	8
α-helix	183-186	4
α-helix	190-195	6
α-helix	201-203	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ADP-ribosylation factor-like protein 8B	A, B	protein	169	Homo sapiens	Q9NVJ2 (AlphaFold model)
Pleckstrin homology domain-containing family M member 1	C, D	protein	196	Homo sapiens	Q9Y4G2 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8JC5_1 ADP-ribosylation factor-like protein 8B (chains A, B)
KEEMELTLVGLQYSGKTTFVNVIASGQFSEDMIPTVGFNMRKVTKGNVTIKIWDIGGLPR
FRSMWERYCRGVNAIVYMIDAADREKIEASRNELHNLLDKPQLQGIPVLVLGNKRDLPNA
LDEKQLIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHSKSRRS

Sequence of entity 2 (C, D), FASTA

>8JC5_2 Pleckstrin homology domain-containing family M member 1 (chains C, D)
DPQAAIPVIKKKLVGSVKALQKQYVSLDTVVTSEDGDANTMCSALEAVFIHGLHAKHIRA
EAGGKRKKSAHQKPLPQPVFWPLLKAVTHKHIISELEHLTFVNTDVGRCRAWLRLALNDG
LMECYLKLLLQEQARLHEYYQPTALLRDAEEGEFLLSFLQGLTSLSFELSYKSAILNEWT
LTPLALSGLCPLSELD

Ligands and cofactors

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

Primary citation

Mechanistic Insights into the Interactions of Arl8b with the RUN Domains of PLEKHM1 and SKIP. Qiu, X., Li, Y., Wang, Y. et al. J Mol Biol (2023) 435:168293-168293. DOI 10.1016/j.jmb.2023.168293 · PubMed

Other PDB entries of the same protein (UniProt Q9NVJ2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8JCA 1.65 Å, Cyrstal structure of SKIP RUN domain in complex with GTP-bound Arl8b(Q75L)
2AL7 1.85 Å, Structure Of Human ADP-Ribosylation Factor-Like 10C

Browse structure collections

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