4P2A: Mouse VPS26A

Structure of mouse VPS26A bound to rat SNX27 PDZ domain. Determined by X-ray diffraction at 2.7 Å resolution. Released 3 Sept 2014.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Mus musculus, Rattus norvegicus
Chains: 2
Atoms: 3,109
Mol. weight: 49.34 kDa
Ligands: HG
Released: 3 Sept 2014

Explore 4P2A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4P2A contains 3 α-helices and 38 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: 1 helix, 29 β-strands

Element	Residues	Length	Sheet
β-strand	11-18	8	1
β-strand	26-30	5	2
β-strand	36-40	5	2
β-strand	41-42	2	3
β-strand	48-56	9	1
β-strand	63-65	3	4
β-strand	67-77	11	5
β-strand	86-96	11	5
β-strand	99-101	3	4
β-strand	105-111	7	1
β-strand	121-122	2	5
β-strand	127-137	11	5
β-strand	143-149	7	5
β-strand	150-151	2	3
β-strand	154-156	3	6
β-strand	164-169	6	7
β-strand	174-180	7	7
β-strand	184-186	3	8
β-strand	190-200	11	7
β-strand	204-216	13	9
β-strand	219	1	10
β-strand	222	1	10
β-strand	225-236	12	9
β-strand	246-251	6	7
α-helix	252-254	3
β-strand	261-264	4	9
β-strand	268-280	13	9
β-strand	285-292	8	9
β-strand	293-295	3	8
β-strand	296-297	2	6

Chain B: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	41-47	7	11
β-strand	55-58	4	11
β-strand	65-66	2	6
β-strand	68-70	3	12
β-strand	73-75	3	12
β-strand	79-84	6	11
α-helix	89-93	5
β-strand	100-104	5	11
β-strand	107-108	2	11
α-helix	114-121	8
β-strand	127-133	7	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 26A	A	protein	327	Mus musculus	P40336 (AlphaFold model)
Sorting nexin-27	B	protein	101	Rattus norvegicus	Q8K4V4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4P2A_1 Vacuolar protein sorting-associated protein 26A (chains A)
MHHHHHHMGPICEIDVALNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPG
KRLEHQGIRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYES
YIGANVRLRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEY
NKSKYHLKDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDGAP
VKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDEEDRRYFKQQEIILWRKAPE
KLRKQRTNFHQRFESPDSQASAEQPEM

Sequence of entity 2 (B), FASTA

>4P2A_2 Sorting nexin-27 (chains B)
GSHGGSPRVVRIVKSESGYGFNVRGQVSEGGQLRSINGELYAPLQHVSAVLPGGAADRAG
VRKGDRILEVNGVNVEGATHKQVVDLIRAGEKELILTVLSV

Ligands and cofactors

ID	Name	Formula	Copies
HG	Mercury (II) ion	Hg	2

Primary citation

A unique PDZ domain and arrestin-like fold interaction reveals mechanistic details of endocytic recycling by SNX27-retromer. Gallon, M., Clairfeuille, T., Steinberg, F. et al. Proc Natl Acad Sci U S A (2014) 111:e3604. DOI 10.1073/pnas.1410552111 · PubMed

Other PDB entries of the same protein (UniProt P40336 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7U6F 4.9 Å, Mouse retromer (VPS26/VPS35/VPS29) heterotrimers
6VAC 5.7 Å, Mouse retromer (VPS26/VPS35/VPS29) heterotrimer

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