5F0P: Retromer VPS26-VPS35 subunits

Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled). Determined by X-ray diffraction at 2.78 Å resolution. Released 7 Dec 2016.

Method: X-ray diffraction
Resolution: 2.78 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,630
Mol. weight: 114.93 kDa
Ligands: ZN
Released: 7 Dec 2016

Explore 5F0P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5F0P contains 50 α-helices and 33 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: 31 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	14-36	23
α-helix	39-50	12
α-helix	51-54	4
α-helix	60-86	27
α-helix	90-91	2
α-helix	94-97	4
α-helix	98-100	3
α-helix	104-121	18
α-helix	123-125	3
α-helix	126-136	11
α-helix	137-139	3
β-strand	140	1	1
α-helix	143-156	14
α-helix	176-196	21
α-helix	197-199	3
α-helix	206-228	23
α-helix	235-237	3
α-helix	238-242	5
α-helix	243-252	10
α-helix	256-269	14
α-helix	272-277	6
α-helix	279-287	9
α-helix	295-310	16
α-helix	324-338	15
α-helix	344-361	18
α-helix	366-382	17
α-helix	385-387	3
α-helix	393-408	16
α-helix	413-416	4
α-helix	423-427	5
α-helix	430-446	17
α-helix	454-468	15

Chain B: 7 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	12-18	7	2
β-strand	26-30	5	3
α-helix	32-34	3
β-strand	36-42	7	3
β-strand	48-56	9	2
β-strand	59	1	4
β-strand	61	1	4
β-strand	63-65	3	5
β-strand	68-78	11	3
α-helix	82-84	3
β-strand	86-96	11	3
β-strand	99-101	3	5
β-strand	105-111	7	2
β-strand	121-122	2	3
β-strand	126-136	11	3
β-strand	143-151	9	3
β-strand	155	1	6
α-helix	162-163	2
β-strand	164-170	7	7
β-strand	174-180	7	7
β-strand	184-186	3	8
β-strand	190-200	11	7
β-strand	204-217	14	1
β-strand	224-237	14	1
β-strand	245-251	7	7
α-helix	252-255	4
α-helix	257-260	4
β-strand	261-264	4	1
β-strand	268-280	13	1
β-strand	285-292	8	1
β-strand	293-295	3	8
α-helix	296	1
β-strand	297	1	6
α-helix	298-299	2

Chain C: 11 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	14-17	4
α-helix	18-22	5
α-helix	24-25	2
β-strand	29-39	11	9
α-helix	42-44	3
β-strand	46-55	10	9
β-strand	64-70	7	9
α-helix	71-84	14
α-helix	89-92	4
α-helix	97-99	3
α-helix	108-110	3
α-helix	112-130	19
α-helix	133-136	4
α-helix	139-146	8

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	554-556	3	1
α-helix	557	1
β-strand	558-559	2	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 35	A	protein	462	Homo sapiens	Q96QK1 (AlphaFold model)
Vacuolar protein sorting-associated protein 26A	B	protein	321	Homo sapiens	O75436 (AlphaFold model)
Sorting nexin-3	C	protein	167	Homo sapiens	O60493 (AlphaFold model)
Natural resistance-associated macrophage protein 2	D	protein	18	Homo sapiens	P49281 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5F0P_1 Vacuolar protein sorting-associated protein 35 (chains A)
GAMGSKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELRTSMLSPKSYYELYM
AISDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVKSFPQSRKD
ILKDLVEMCRGVQHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFA
EMNKLWVRMQHQGHSRDREKRERERQELRILVGTNLVRLSQLEGVNVERYKQIVLTGILE
QVVNCRDALAQEYLMECIIQVFPDEFHLQTLNPFLRACAELHQNVNVKNIIIALIDRLAL
FAHREDGPGIPADIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLINLAMKCYPDRVDY
VDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKHFHPLFEYF
DYESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQD

Sequence of entity 2 (B), FASTA

>5F0P_2 Vacuolar protein sorting-associated protein 26A (chains B)
MSFLGGFFGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPG
KRLEHQGIRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYES
YIGANVRLRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEY
NKSKYHLKDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDGAP
VKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDEEDRRYFKQQEIILWRKAPE
KLRKQRTNFHQRFESPESQAS

Sequence of entity 3 (C), FASTA

>5F0P_3 Sorting nexin-3 (chains C)
GAMGSMAETVADTRRLITKPQNLNDAYGPPSNFLEIDVSNPQTVGVGRGRFTTYEIRVKT
NLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDNFI
EERKQGLEQFINKVAGHPLAQNERCLHMFLQDEIIDKSYTPSKIRHA

Sequence of entity 4 (D), FASTA

>5F0P_4 Natural resistance-associated macrophage protein 2 (chains D)
TAQPELYLMNTMSHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (SO4, GOL, EDO) are not listed.

Primary citation

Structural Mechanism for Cargo Recognition by the Retromer Complex. Lucas, M., Gershlick, D.C., Vidaurrazaga, A. et al. Cell (2016) 167:1623-1635.e14. DOI 10.1016/j.cell.2016.10.056 · PubMed

Other PDB entries of the same protein (UniProt Q96QK1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8R0J 2.4 Å, Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl…
8R02 2.5 Å, Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl…
5OSI 2.52 Å, Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176)
5F0J 2.7 Å, Structure of retromer VPS26-VPS35 subunits bound to SNX3
2R17 2.8 Å, Functional architecture of the retromer cargo-recognition complex
5F0K 3.07 Å, Structure of VPS35 N terminal region
5F0M 3.1 Å, Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled)
8RKS 3.1 Å, Structure of VPS29-VPS35 bound to the LFa motif R21 of Fam21.
9Q8M 3.13 Å, VPS35-VPS26-SNX12 Complex
5F0L 3.2 Å, Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1
5OSH 4.3 Å, Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236)
7BLN 8.9 Å, VPS35/VPS29 arch of metazoan membrane-assembled retromer:SNX3 complex modelled with…

Browse structure collections

About this viewer

MolViewer shows 5F0P directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.