7C7J: SHANK3 SPN domain

Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(G12V,Q63E). Determined by X-ray diffraction at 2.39 Å resolution. Released 5 May 2021.

Method: X-ray diffraction
Resolution: 2.39 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,235
Mol. weight: 61.65 kDa
Ligands: MG, CA, GTP
Released: 5 May 2021

Explore 7C7J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7C7J contains 27 α-helices and 34 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
α-helix	16-25	10
β-strand	37-46	10	1
β-strand	49-58	10	1
α-helix	65-74	10
β-strand	77-83	7	1
α-helix	87-91	5
α-helix	93-104	12
β-strand	111-116	6	1
α-helix	128-137	10
β-strand	142-145	4	1
β-strand	147	1	2
β-strand	152	1	2
α-helix	155-165	11

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	3
α-helix	16-25	10
β-strand	37-45	9	3
β-strand	50-58	9	3
α-helix	59	1
α-helix	65-74	10
β-strand	77-83	7	3
α-helix	87-91	5
α-helix	93-103	11
β-strand	111-116	6	3
α-helix	121-123	3
α-helix	128-137	10
β-strand	142-145	4	3
β-strand	147	1	4
β-strand	152	1	4
α-helix	155-166	12

Chain C: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	1
α-helix	16-18	3
β-strand	20-26	7	1
β-strand	31	1	5
α-helix	32-43	12
α-helix	50-52	3
β-strand	53-57	5	1
α-helix	58-59	2
β-strand	60	1	6
β-strand	63	1	6
β-strand	66-67	2	1
α-helix	68-69	2
β-strand	73	1	5
α-helix	74-76	3
α-helix	78-80	3
β-strand	87-92	6	1

Chain D: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	3
α-helix	16-18	3
β-strand	20-26	7	3
β-strand	31	1	7
α-helix	32-43	12
α-helix	50-52	3
β-strand	53-57	5	3
β-strand	60	1	8
β-strand	63	1	8
α-helix	64-65	2
β-strand	66-67	2	3
α-helix	68-69	2
β-strand	73	1	7
α-helix	74-76	3
β-strand	87-92	6	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rap-1b	A, B	protein	167	Homo sapiens	P61224 (AlphaFold model)
SH3 and multiple ankyrin repeat domains protein 3	C, D	protein	99	Homo sapiens	Q9BYB0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7C7J_1 Ras-related protein Rap-1b (chains A, B)
MREYKLVVLGSVGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAG
TEEFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDL
EDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR

Sequence of entity 2 (C, D), FASTA

>7C7J_2 SH3 and multiple ankyrin repeat domains protein 3 (chains C, D)
MDGPGASAVVVRVGIPDLQQTKCLRLDPAAPVWAAKQRVLCALNHSLQDALNYGLFQPPS
RGRAGKFLDEERLLQEYPPNLDTPLPYLEFRYKRRVYAQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
CA	Calcium ion	Ca	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

Primary citation

Mechanistic Insights into the Interactions of Ras Subfamily GTPases with the SPN Domain of Autism-associated SHANK3. Xu, X.L., Liu, J.P., Wang, Y.L. et al. Chin J Chem (2020) 38:1635-1641. DOI 10.1002/cjoc.202000278

Other PDB entries of the same protein (UniProt P61224 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HDO 1.67 Å, Crystal structure of the binary Complex of KRIT1 bound to the Rap1 GTPase
6OQ4 1.75 Å, Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi1
6OQ3 1.85 Å, Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi2
6UZK 1.92 Å, Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi6
4DXA 1.95 Å, Co-crystal structure of Rap1 in complex with KRIT1
4HDQ 1.95 Å, Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and the…
8SU8 2.01 Å, Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative…
8T09 2.15 Å, Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative…
3CF6 2.2 Å, Structure of Epac2 in complex with cyclic-AMP and Rap
8T7V 2.25 Å, Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative…
7C7I 2.28 Å, Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(E30D,K31E)
4MH0 2.4 Å, Selective activation of Epac1 and Epac2

Browse structure collections

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