7R2T: Synaptojanin-2-binding protein,Annexin

SYNJ2BP complex with a phosphorylated Vangl2 peptide at the P-1 position. Determined by X-ray diffraction at 2.5 Å resolution. Released 17 May 2023.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,332
Mol. weight: 49.29 kDa
Ligands: CA
Released: 17 May 2023

Explore 7R2T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R2T contains 22 α-helices and 9 β-strands across 2 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: 22 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	8-17	10	1
β-strand	19	1	2
β-strand	22	1	2
β-strand	25-29	5	1
β-strand	42-47	6	1
α-helix	52-56	5
β-strand	64-68	5	1
β-strand	71-72	2	1
α-helix	78-86	9
β-strand	91-100	10	1
α-helix	118-129	12
α-helix	136-143	8
α-helix	148-162	15
α-helix	166-173	8
α-helix	176-186	11
α-helix	189-201	13
α-helix	208-217	10
α-helix	220-234	15
α-helix	238-245	8
α-helix	248-258	11
α-helix	262-264	3
α-helix	271-284	14
α-helix	293-302	10
α-helix	305-318	14
α-helix	323-328	6
α-helix	333-362	30
α-helix	368-378	11
α-helix	383-394	12
α-helix	398-405	8
α-helix	408-418	11

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	204-205	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptojanin-2-binding protein,Annexin	A	protein	422	Homo sapiens	P57105 (AlphaFold model)
Vangle2 peptide binding motif with the P-1 phosphrylated	B	protein	9	Homo sapiens	Q9ULK5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7R2T_1 Synaptojanin-2-binding protein,Annexin (chains A)
QGSHMDYLVTEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIYVSRIKENGAAALDGRLQ
EGDKILSVNGQDLKNLLHQDAVDLFRNAGYAVSLRVQHRLQVQGSAYGSVKAYTNFDAER
DALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSGHLET
VILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEK
DIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIM
TERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDS
MKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGG
DD

Sequence of entity 2 (B), FASTA

>7R2T_2 Vangle2 peptide binding motif with the P-1 phosphrylated (chains B)
MRLQSETSV

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	5

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

Primary citation

PDZome-wide and structural characterization of the PDZ-binding motif of VANGL2. Montserrat-Gomez, M., Gogl, G., Carrasco, K. et al. Biochim Biophys Acta Proteins Proteom (2024) 1872:140989-140989. DOI 10.1016/j.bbapap.2023.140989 · PubMed

Other PDB entries of the same protein (UniProt P57105 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2JIK 1.35 Å, Crystal structure of PDZ domain of Synaptojanin-2 binding protein
2JIN 1.5 Å, Crystal structure of PDZ domain of Synaptojanin-2 binding protein
7P73 1.85 Å, The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1
7P74 1.9 Å, The PDZ domain of SYNJ2BP complexed with the phosphorylated PDZ-binding motif of RSK1
8AEL 2.2 Å, SYNJ2BP complex with a synthetic Vangl2 peptide (3mer).
7PC9 2.4 Å, The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1
7R2M 2.4 Å, SYNJ2BP complex with a synthetic Vangl2 peptide (9mer).
2ENO Solution structure of the PDZ domain from human Synaptojanin 2 binding protein

Browse structure collections

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