5F0M: Retromer VPS26-VPS35 subunits

Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled). Determined by X-ray diffraction at 3.1 Å resolution. Released 7 Dec 2016.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,544
Mol. weight: 114.4 kDa
Released: 7 Dec 2016

Explore 5F0M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5F0M contains 49 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: 29 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	14-35	22
α-helix	39-50	12
α-helix	51-54	4
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	143-156	14
α-helix	176-196	21
α-helix	206-215	10
α-helix	217-228	12
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	295-311	17
α-helix	324-338	15
α-helix	344-361	18
α-helix	366-382	17
α-helix	393-408	16
α-helix	412-417	6
α-helix	423-427	5
α-helix	430-446	17
α-helix	454-468	15

Chain B: 8 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	12-18	7	2
α-helix	25	1
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	65	1	5
β-strand	67-78	12	3
α-helix	82-84	3
β-strand	86-96	11	3
β-strand	99	1	5
β-strand	105-111	7	2
β-strand	121-122	2	3
β-strand	126-137	12	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: 10 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
β-strand	46-55	10	9
β-strand	64-70	7	9
α-helix	71-84	14
α-helix	89-92	4
α-helix	98-100	3
α-helix	108-110	3
α-helix	112-130	19
α-helix	133-136	4
α-helix	139-146	8

Chain D: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	554-556	3	1
α-helix	557	1
β-strand	558-559	2	7
α-helix	560	1

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

>5F0M_1 Vacuolar protein sorting-associated protein 35 (chains A)
GAMGSKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELRTSMLSPKSYYELYM
AISDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVKSFPQSRKD
ILKDLVEMCRGVQHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFA
EMNKLWVRMQHQGHSRDREKRERERQELRILVGTNLVRLSQLEGVNVERYKQIVLTGILE
QVVNCRDALAQEYLMECIIQVFPDEFHLQTLNPFLRACAELHQNVNVKNIIIALIDRLAL
FAHREDGPGIPADIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLINLAMKCYPDRVDY
VDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKHFHPLFEYF
DYESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQD

Sequence of entity 2 (B), FASTA

>5F0M_2 Vacuolar protein sorting-associated protein 26A (chains B)
MSFLGGFFGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPG
KRLEHQGIRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYES
YIGANVRLRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEY
NKSKYHLKDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDGAP
VKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDEEDRRYFKQQEIILWRKAPE
KLRKQRTNFHQRFESPESQAS

Sequence of entity 3 (C), FASTA

>5F0M_3 Sorting nexin-3 (chains C)
GAMGSMAETVADTRRLITKPQNLNDAYGPPSNFLEIDVSNPQTVGVGRGRFTTYEIRVKT
NLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDNFI
EERKQGLEQFINKVAGHPLAQNERCLHMFLQDEIIDKSYTPSKIRHA

Sequence of entity 4 (D), FASTA

>5F0M_4 Natural resistance-associated macrophage protein 2 (chains D)
TAQPELYLLNTMSHHHHH

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
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…

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