9JKA: Human VANGL2

Human VANGL2 in complex with a PK1 peptide (residues 745-790). Determined by electron microscopy at 2.5 Å resolution. Released 25 Dec 2024.

Method: Electron microscopy
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 6
Atoms: 17,820
Mol. weight: 362.24 kDa
Released: 25 Dec 2024

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

Secondary structure: helices and β-sheets

9JKA contains 120 α-helices and 84 β-strands across 6 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.

Chains A, B, C, D, E and F: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	110-133	24
α-helix	139-140	2
α-helix	143-167	25
β-strand	173-174	2	1
α-helix	180-200	21
α-helix	201-205	5
α-helix	212-234	23
α-helix	235-239	5
β-strand	246-252	7	2
β-strand	258-263	6	2
β-strand	267	1	3
α-helix	268-282	15
β-strand	284	1	4
α-helix	285-286	2
α-helix	327-335	9
α-helix	340-367	28
β-strand	371-372	2	5
α-helix	387-395	9
α-helix	399-408	10
α-helix	417-429	13
α-helix	434-442	9
β-strand	446	1	4
α-helix	447-449	3
α-helix	457-459	3
β-strand	460-464	5	2
β-strand	471	1	3
α-helix	472	1
β-strand	477-481	5	2
β-strand	486-493	8	2
α-helix	494-496	3
β-strand	497-498	2	6
β-strand	499-502	4	7
α-helix	506-508	3
β-strand	511-512	2	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vang-like protein 2	A, B, C, D, E, F	protein	527	Homo sapiens	Q9ULK5 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>9JKA_1 Vang-like protein 2 (chains A, B, C, D, E, F)
GPSRATMDTESQYSGYSYKSGHSRSSRKHRDRRDRHRSKSRDGGRGDKSVTIQAPGEPLL
DNESTRGDERDDNWGETTTVVTGTSEHSISHDDLTRIAKDMEDSVPLDCSRHLGVAAGAT
LALLSFLTPLAFLLLPPLLWREELEPCGTACEGLFISVAFKLLILLLGSWALFFRRPKAS
LPRVFVLRALLMVLVFLLVVSYWLFYGVRILDARERSYQGVVQFAVSLVDALLFVHYLAV
VLLELRQLQPQFTLKVVRSTDGASRFYNVGHLSIQRVAVWILEKYYHDFPVYNPALLNLP
KSVLAKKVSGFKVYSLGEENSTNNSTGQSRAVIAAAARRRDNSHNEYYYEEAEHERRVRK
RRARLVVAVEEAFTHIKRLQEEEQKNPREVMDPREAAQAIFASMARAMQKYLRTTKQQPY
HTMESILQHLEFCITHDMTPKAFLERYLAAGPTIQYHKERWLAKQWTLVSEEPVTNGLKD
GIVFLLKRQDFSLVVSTKKVPFFKLSEEFVDPKSHKFVMRLQSETSV

Primary citation

Structural basis of human VANGL-PRICKLE interaction. Song, Y., Jian, S., Teng, J. et al. Nat Commun (2025) 16:132-132. DOI 10.1038/s41467-024-55396-3 · PubMed

Other PDB entries of the same protein (UniProt Q9ULK5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

35UG 1.95 Å, Human DVL2 PDZ domain in complex with Vangl2
6XA6 1.95 Å, Crystal Structure of Human Scribble PDZ3:Vangl2 Complex
6XA8 2.2 Å, Crystal Structure of Human Scribble PDZ1:Vangl2 complex
7R2M 2.4 Å, SYNJ2BP complex with a synthetic Vangl2 peptide (9mer).
6XA7 2.5 Å, Crystal Structure of Human Scribble PDZ2:Vangl2 complex
7R2T 2.5 Å, SYNJ2BP complex with a phosphorylated Vangl2 peptide at the P-1 position.
9JK7 2.9 Å, Human VANGL2 hexamer

Browse structure collections

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