7R2M: Synaptojanin-2-binding protein,Annexin

SYNJ2BP complex with a synthetic Vangl2 peptide (9mer). Determined by X-ray diffraction at 2.4 Å resolution. Released 17 May 2023.

Method
X-ray diffraction
Resolution
2.4 Å
Organism
Homo sapiens
Chains
4
Atoms
6,861
Mol. weight
101.61 kDa
Ligands
PE4, CA
Released
17 May 2023

Explore 7R2M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R2M contains 44 α-helices and 18 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: 22 helices, 8 β-strands

ElementResiduesLengthSheet
β-strand8-17103
β-strand1914
β-strand2214
β-strand25-2953
β-strand42-4763
α-helix52-565
β-strand64-6853
β-strand71-7223
α-helix78-869
β-strand91-100103
α-helix118-13013
α-helix136-1438
α-helix148-16215
α-helix166-1738
α-helix176-18611
α-helix189-20012
α-helix208-21710
α-helix220-23415
α-helix238-2458
α-helix248-25811
α-helix262-2665
α-helix271-28313
α-helix293-30210
α-helix305-31814
α-helix323-3308
α-helix333-36230
α-helix368-37710
α-helix383-39412
α-helix398-4058
α-helix408-41811
Chains B and E: 0 helices, 1 β-strand
ElementResiduesLengthSheet
β-strand204-20523
Chain D: 22 helices, 8 β-strands
ElementResiduesLengthSheet
β-strand8-17101
β-strand1912
β-strand2212
β-strand25-2951
β-strand42-4761
α-helix52-565
β-strand64-6851
β-strand71-7221
α-helix78-869
β-strand91-100101
α-helix118-13013
α-helix136-1438
α-helix148-16215
α-helix166-1738
α-helix176-18611
α-helix189-20113
α-helix208-21710
α-helix220-23415
α-helix238-2458
α-helix248-25811
α-helix262-2643
α-helix271-28414
α-helix293-30210
α-helix305-31814
α-helix323-3308
α-helix333-36129
α-helix368-37811
α-helix383-39412
α-helix398-4058
α-helix408-41811

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Synaptojanin-2-binding protein,AnnexinA, Dprotein422Homo sapiensP57105 (AlphaFold model)
Vangl2 peptideB, Eprotein24Homo sapiensQ9ULK5 (AlphaFold model)
Sequence of entity 1 (A, D), FASTA
>7R2M_1 Synaptojanin-2-binding protein,Annexin (chains A, D)
QGSHMDYLVTEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIYVSRIKENGAAALDGRLQ
EGDKILSVNGQDLKNLLHQDAVDLFRNAGYAVSLRVQHRLQVQGSAYGSVKAYTNFDAER
DALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSGHLET
VILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEK
DIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIM
TERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDS
MKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGG
DD
Sequence of entity 2 (B, E), FASTA
>7R2M_2 Vangl2 peptide (chains B, E)
GSGSGGMRLQSETSVMRLQSETSV

Ligands and cofactors

IDNameFormulaCopies
PE42-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-etha…C16 H34 O81
CACalcium ionCa9

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:

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