6XA8: Human Scribble PDZ1:Vangl2 complex

Crystal Structure of Human Scribble PDZ1:Vangl2 complex. Determined by X-ray diffraction at 2.2 Å resolution. Released 24 Mar 2021.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 1,629
Mol. weight: 27.68 kDa
Ligands: PO4
Released: 24 Mar 2021

Explore 6XA8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XA8 contains 8 α-helices and 22 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: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	717-720	4
β-strand	721-732	12	1
β-strand	740-743	4	1
β-strand	746	1	2
β-strand	752	1	3
β-strand	755	1	3
β-strand	758-763	6	1
α-helix	768-772	5
α-helix	778	1
β-strand	779-783	5	1
β-strand	786-787	2	1
β-strand	792	1	2
α-helix	793-801	9
β-strand	806-814	9	1

Chain B: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	718-720	3
β-strand	721-732	12	1
β-strand	740-743	4	1
β-strand	746	1	4
β-strand	752	1	5
β-strand	755	1	5
β-strand	758-763	6	1
α-helix	768-772	5
α-helix	778	1
β-strand	779-783	5	1
β-strand	786-787	2	1
β-strand	792	1	4
α-helix	793-801	9
β-strand	806-814	9	1

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	208-210	3	1

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	388-390	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein scribble homolog	A, B	protein	122	Homo sapiens	Q14160 (AlphaFold model)
C-terminal peptide of Vangl2	C, D	protein	7	Homo sapiens	Q9ULK5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6XA8_1 Protein scribble homolog (chains A, B)
GPLGSSAPSVKGVSFDQANNLLIEPARIEEEELTLTILRQTGGLGISIAGGKGSTPYKGD
DEGIFISRVSEEGPAARAGVRVGDKLLEVNGVALQGAEHHEAVEALRGAGTAVQMRVWRE
RM

Sequence of entity 2 (C, D), FASTA

>6XA8_2 C-terminal peptide of Vangl2 (chains C, D)
LQSETSV

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	4

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

Primary citation

Structural basis of the human Scribble-Vangl2 association in health and disease. How, J.Y., Stephens, R.K., Lim, K.Y.B. et al. Biochem J (2021) 478:1321-1332. DOI 10.1042/BCJ20200816 · PubMed

Other PDB entries of the same protein (UniProt Q14160 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6MYE 1.1 Å, Crystal structure of human Scribble PDZ1 domain in complex with internal PDZ binding…
6EEY 1.15 Å, Crystal structure of human Scribble PDZ4 R1110G Mutant
2W4F 1.3 Å, Crystal structure of the first PDZ domain of human SCRIB1
6MS1 1.35 Å, Crystal structure of the human Scribble PDZ1 domain bound to the PDZ-binding motif of APC
6MYF 1.6 Å, Crystal structure of free human Scribble PDZ1 domain
5VWI 1.75 Å, Crystal structure of human Scribble PDZ1:Beta-PIX complex
7QRS 1.77 Å, Structural insight into the Scribble PDZ domains interaction with the oncogenic Human…
7QS9 1.8 Å, Structural basis on the interaction of Scribble PDZ domains with the Tick Born…
7QSB 1.84 Å, Structural basis on the interaction of Scribble PDZ domains with the Tick Born…
7QS8 1.85 Å, Structural insight into the Scribble PDZ domains interaction with the oncogenic Human…
7QRT 1.9 Å, Structural insight into the Scribble PDZ domains interaction with the oncogenic Human…
7QTP 1.9 Å, Structural biology of the NS1 avian influenza protein subversion on the Scribble cell…

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