7YKI: MAGI2 PDZ0-GK domain

Crystal structure of MAGI2 PDZ0-GK domain in complex with phospho-SAPAP1 GBR3 peptide. Determined by X-ray diffraction at 2.0 Å resolution. Released 2 Aug 2023.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Mus musculus
Chains: 4
Atoms: 3,317
Mol. weight: 56.08 kDa
Ligands: PO4
Released: 2 Aug 2023

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

Secondary structure: helices and β-sheets

7YKI contains 23 α-helices and 36 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	16-21	6	1
β-strand	32-34	3	1
α-helix	36-38	3
β-strand	40	1	2
β-strand	42-44	3	1
β-strand	53-54	2	1
α-helix	55	1
β-strand	58	1	1
α-helix	64	1
β-strand	65-69	5	1
β-strand	72-73	2	1
α-helix	79-87	9
α-helix	89-90	2
β-strand	93-98	6	1
β-strand	101	1	3
β-strand	104	1	3
β-strand	107	1	2
α-helix	108-113	6
α-helix	121-135	15
β-strand	140-141	2	4
α-helix	144-145	2
β-strand	151	1	5
β-strand	155	1	5
β-strand	156-157	2	4
α-helix	160-168	9
β-strand	172-178	7	4
β-strand	181-186	6	4
α-helix	187-189	3

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	-1-5	7

Chain C: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	16-21	6	6
β-strand	32-34	3	6
α-helix	36-38	3
β-strand	40	1	7
β-strand	42-44	3	6
β-strand	53-54	2	6
α-helix	55	1
β-strand	58	1	6
α-helix	64	1
β-strand	65-69	5	6
β-strand	72-73	2	6
α-helix	79-87	9
α-helix	89-90	2
β-strand	93-98	6	6
β-strand	101	1	8
β-strand	104	1	8
β-strand	107	1	7
α-helix	108-113	6
α-helix	121-134	14
α-helix	138-139	2
β-strand	140-141	2	9
α-helix	144-145	2
β-strand	151	1	10
β-strand	155	1	10
β-strand	156-157	2	9
α-helix	160-169	10
β-strand	172-178	7	9
β-strand	181-186	6	9
α-helix	187-189	3

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	-1-4	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2	A, C	protein	234	Mus musculus	Q9WVQ1 (AlphaFold model)
SAPAP1	B, D	protein	14	Mus musculus	Q9D415 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7YKI_1 Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 (chains A, C)
GPGSSHWTSKVHESVIGRNPEGQLGFELKGGAENGQFPYLGEVKPGKVAYESGSKLVSEE
LLLEVNETPVAGLTIRDVLAVIKHCKDPLRLKCVKQGGIVDKDLRHYLNLRFQKGSVDHE
LQQIIRDNLYLRTVPCTTRPHKEGEVPGVDYIFITVEEFMELEKSGALLESGTYEDNYYG
TPKPPAEPAPLLNVTDQILPGATPSAEGKRKRNKSVTNMEKASIEPPEEEEEER

Sequence of entity 2 (B, D), FASTA

>7YKI_2 SAPAP1 (chains B, D)
IRSHSYLRAVSEVS

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2

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

Primary citation

Phosphorylation-dependent recognition of diverse protein targets by the cryptic GK domain of MAGI MAGUKs. Zhang, M., Cao, A., Lin, L. et al. Sci Adv (2023) 9:eadf3295-eadf3295. DOI 10.1126/sciadv.adf3295 · PubMed

Other PDB entries of the same protein (UniProt Q9WVQ1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6JJZ 1.65 Å, Crystal Structure of MAGI2 and Dendrin complex
6KKG 2.15 Å, Crystal structure of MAGI2-Dendrin complex
7YKG 2.16 Å, Crystal structure of MAGI2 PDZ0-GK/pSGEF complex
7YKF 2.28 Å, Crystal structure of MAGI2 PDZ0-GK/pEphexin4 complex
7YKH 2.5 Å, Crystal structure of MAGI2 PDZ0-GK domain in complex with phospho-SAPAP1 GBR2 peptide
7D6F 3.0 Å, The crystal structure of ARMS-PBM/MAGI2-PDZ4

Browse structure collections

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