5F0L: Retromer VPS26-VPS35 subunits

Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1. Determined by X-ray diffraction at 3.2 Å resolution. Released 7 Dec 2016.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,638
Mol. weight: 114.94 kDa
Released: 7 Dec 2016

Explore 5F0L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5F0L contains 48 α-helices and 32 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: 29 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	14-36	23
α-helix	39-51	13
α-helix	52-54	3
α-helix	60-86	27
α-helix	90-91	2
α-helix	94-98	5
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	143-157	15
α-helix	176-196	21
α-helix	206-228	23
α-helix	235-237	3
α-helix	238-242	5
α-helix	243-253	11
α-helix	256-269	14
α-helix	272-277	6
α-helix	279-286	8
α-helix	295-310	16
α-helix	324-338	15
α-helix	344-361	18
α-helix	366-382	17
α-helix	393-408	16
α-helix	413-416	4
α-helix	423-427	5
α-helix	430-446	17
α-helix	448-453	6
α-helix	454-468	15

Chain B: 6 helices, 26 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	63-65	3	4
β-strand	68-78	11	3
α-helix	82-84	3
β-strand	85-96	12	3
β-strand	99-101	3	4
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	5
α-helix	156-158	3
α-helix	162-163	2
β-strand	164-170	7	6
β-strand	174-180	7	6
β-strand	184-186	3	7
β-strand	190-200	11	6
β-strand	204-219	16	1
β-strand	222-237	16	1
β-strand	245-251	7	6
α-helix	252-255	4
α-helix	258-260	3
β-strand	261-264	4	1
β-strand	268-280	13	1
β-strand	285-288	4	1
β-strand	291-292	2	1
β-strand	293-295	3	7
β-strand	297	1	5

Chain C: 12 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	8
α-helix	42-44	3
β-strand	46-55	10	8
β-strand	64-70	7	8
α-helix	71-80	10
α-helix	81-85	5
α-helix	89-92	4
α-helix	97-100	4
α-helix	108-110	3
α-helix	112-131	20
α-helix	133-137	5
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	6

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	317	Homo sapiens	O75436 (AlphaFold model)
Sorting nexin-3	C	protein	167	Homo sapiens	O60493 (AlphaFold model)
Natural resistance-associated macrophage protein 2	D	protein	24	Homo sapiens	P49281 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5F0L_1 Vacuolar protein sorting-associated protein 35 (chains A)
GAMGSKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELRTSMLSPKSYYELYM
AISDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVKSFPQSRKD
ILKDLVEMCRGVQHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFA
EMNKLWVRMQHQGHSRDREKRERERQELRILVGTNLVRLSQLEGVNVERYKQIVLTGILE
QVVNCRDALAQEYLMECIIQVFPDEFHLQTLNPFLRACAELHQNVNVKNIIIALIDRLAL
FAHREDGPGIPADIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLINLAMKCYPDRVDY
VDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKHFHPLFEYF
DYESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQD

Sequence of entity 2 (B), FASTA

>5F0L_2 Vacuolar protein sorting-associated protein 26A (chains B)
MSFLGGFFGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPG
KRLEHQGIRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYES
YIGANVRLRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEY
NKSKYHLKDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDGAP
VKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDEEDRRYFKQQEIILWRKAPE
KLRKQRTNFHQRFESPE

Sequence of entity 3 (C), FASTA

>5F0L_3 Sorting nexin-3 (chains C)
GAMGSMAETVADTRRLITKPQNLNDAYGPPSNFLEIDVSNPQTVGVGRGRFTTYEIRVKT
NLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDNFI
EERKQGLEQFINKVAGHPLAQNERCLHMFLQDEIIDKSYTPSKIRHA

Sequence of entity 4 (D), FASTA

>5F0L_4 Natural resistance-associated macrophage protein 2 (chains D)
HLGLTAQPELYLLNTMDADSLVSR

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
5F0P 2.78 Å, Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled)
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
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…

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