9JU1: Helix-loop-helix peptide

Helix-loop-helix peptide (VS42-LR3) in complex with VEGF-A. Determined by X-ray diffraction at 1.45 Å resolution. Released 25 Dec 2024.

Method: X-ray diffraction
Resolution: 1.45 Å
Organisms: synthetic construct, Homo sapiens
Chains: 2
Atoms: 1,281
Mol. weight: 16.78 kDa
Released: 25 Dec 2024

Explore 9JU1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JU1 contains 5 α-helices and 7 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: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	13-16	4
α-helix	17-24	8
β-strand	25	1	1
β-strand	27-34	8	2
α-helix	35-38	4
β-strand	46-48	3	3
β-strand	51-58	8	2
β-strand	60	1	1
β-strand	66-84	19	3
β-strand	88-106	19	3

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-16	15
α-helix	26-42	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VS42-LR3	C	protein	44	synthetic construct
Vascular endothelial growth factor A, long form	A	protein	102	Homo sapiens	P15692 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>9JU1_1 VS42-LR3 (chains C)
CAAELAALEAELAALEGHVEEADFPWGKLNNLIEKLWQLKQACX

Sequence of entity 2 (A), FASTA

>9JU1_2 Vascular endothelial growth factor A, long form (chains A)
GQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLE
CVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD

Primary citation

Structural insights into molecular-targeting helix-loop-helix peptide against vascular endothelial growth factor-A. Michigami, M., Notsu, K., Kamo, M. et al. Biochem Biophys Res Commun (2024) 734:150749. DOI 10.1016/j.bbrc.2024.150749 · PubMed

Other PDB entries of the same protein (UniProt P15692 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MKK 1.32 Å, Disulfide deficient mutant of vascular endothelial growth factor A (C61A and C104A)
9KKU 1.46 Å, Helix-loop-helix peptide (M49) in complex with VEGF-A
4GLN 1.6 Å, Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus…
4GLS 1.6 Å, Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus…
6ZBR 1.6 Å, VEGF-A 13:107 crystallized with 4C bicyclic peptide
6ZFL 1.6 Å, High resolution structure of VEGF-A 12:107 crystallized in tetragonal form
1FLT 1.7 Å, Vegf in complex with domain 2 of the flt-1 receptor
4KZN 1.71 Å, crystal structure of human VEGF-A receptor binding domain
4QAF 1.8 Å, Crystal structure of an engineered lipocalin (Anticalin) in complex with VEGF(8-109)
6Z13 1.8 Å, VEGF-A 13:107 crystallized with 3C bicyclic peptide
6ZCD 1.8 Å, VEGF-A 13:107 crystallized with 1C bicyclic peptide
3QTK 1.85 Å, The crystal structure of chemically synthesized VEGF-A

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