5OSH: Retromer VPS29-VPS35C subunits

Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236). Determined by X-ray diffraction at 4.3 Å resolution. Released 13 Dec 2017.

Method: X-ray diffraction
Resolution: 4.3 Å
Organisms: Homo sapiens, Legionella pneumophila subsp. pneumophila ATCC 43290
Chains: 12
Atoms: 22,276
Mol. weight: 322.5 kDa
Released: 13 Dec 2017

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

Secondary structure: helices and β-sheets

5OSH contains 124 α-helices and 76 β-strands across 12 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: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	7	1	2
β-strand	11	1	3
α-helix	20-25	6
β-strand	31-36	6	1
β-strand	41	1	3
α-helix	43-52	10
β-strand	53-56	4	1
β-strand	72-77	6	4
β-strand	80-85	6	4
α-helix	96-106	11
β-strand	110-112	3	4
β-strand	120-123	4	4
β-strand	128-131	4	4
β-strand	134	1	2
β-strand	149-155	7	1
β-strand	160-168	9	1
β-strand	171-179	9	1

Chain B: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	486-497	12
α-helix	503-517	15
α-helix	525-545	21
α-helix	553-572	20
α-helix	578-594	17
α-helix	600-617	18
α-helix	621-637	17
α-helix	643-658	16
α-helix	663-672	10
α-helix	675-677	3
α-helix	693-708	16
α-helix	713-732	20
α-helix	740-753	14
α-helix	754-756	3
α-helix	761-779	19

Chain C: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	12-26	15
α-helix	30-45	16
α-helix	51-60	10
α-helix	62-65	4
α-helix	85-89	5
α-helix	104-120	17
α-helix	125-133	9
α-helix	136-145	10
β-strand	155	1	5
β-strand	158	1	5
β-strand	165-166	2	6
β-strand	174-175	2	6
α-helix	184-203	20
α-helix	211-219	9

Chain D: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
β-strand	7	1	8
β-strand	11	1	9
α-helix	20-25	6
β-strand	33-36	4	7
β-strand	41	1	9
α-helix	43-52	10
β-strand	55-57	3	7
β-strand	73-77	5	10
β-strand	80-84	5	10
α-helix	96-106	11
β-strand	110-112	3	10
β-strand	120-124	5	10
β-strand	127-131	5	10
β-strand	134	1	8
β-strand	140	1	11
β-strand	143	1	11
β-strand	149-154	6	7
β-strand	160-168	9	7
β-strand	171-179	9	7

Chain E: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	491-493	3
α-helix	494-498	5
α-helix	503-517	15
α-helix	525-527	3
α-helix	529-545	17
α-helix	553-572	20
α-helix	578-594	17
α-helix	599-617	19
α-helix	621-637	17
α-helix	643-659	17
α-helix	663-673	11
α-helix	676-679	4
β-strand	681	1	12
β-strand	689	1	12
α-helix	693-706	14
α-helix	713-732	20
α-helix	740-751	12
α-helix	758	1
α-helix	761-776	16

Chain F: 13 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	12-28	17
α-helix	30-44	15
α-helix	51-59	9
α-helix	62-68	7
α-helix	70-72	3
α-helix	82-84	3
α-helix	85-89	5
α-helix	104-120	17
α-helix	125-133	9
α-helix	136-145	10
β-strand	155	1	13
β-strand	158	1	13
β-strand	165-166	2	14
α-helix	172-173	2
β-strand	174-175	2	14
α-helix	184-202	19
α-helix	213-219	7

Chain G: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	15
α-helix	20-25	6
β-strand	33-36	4	15
α-helix	44-50	7
β-strand	55-58	4	15
β-strand	73-76	4	16
β-strand	81-84	4	16
α-helix	96-106	11
β-strand	110-112	3	16
β-strand	120-123	4	16
β-strand	128-131	4	16
β-strand	150-155	6	15
β-strand	159-165	7	15
β-strand	174-180	7	15

Chain H: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	494-498	5
α-helix	503-517	15
α-helix	525-545	21
α-helix	553-570	18
α-helix	571-574	4
α-helix	578-594	17
α-helix	599-617	19
α-helix	621-637	17
α-helix	643-658	16
α-helix	663-677	15
β-strand	682	1	17
β-strand	688	1	17
α-helix	693-708	16
α-helix	713-731	19
α-helix	740-753	14
α-helix	761-775	15

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 29	A, D, G, J	protein	182	Homo sapiens	Q9UBQ0 (AlphaFold model)
Vacuolar protein sorting-associated protein 35	B, E, H, K	protein	299	Homo sapiens	Q96QK1 (AlphaFold model)
Interaptin	C, F, I, L	protein	223	Legionella pneumophila subsp. pneumophila ATCC 43290	A0ABF7PFW6 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>5OSH_1 Vacuolar protein sorting-associated protein 29 (chains A, D, G, J)
MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVR
GDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFE
AFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYK
KP

Sequence of entity 2 (B, E, H, K), FASTA

>5OSH_2 Vacuolar protein sorting-associated protein 35 (chains B, E, H, K)
EDFADEQSLVGRFIHLLRSEDPDQQYLILNTARKHFGAGGNQRIRFTLPPLVFAAYQLAF
RYKENSKVDDKWEKKCQKIFSFAHQTISALIKAELAELPLRLFLQGALAAGEIGFENHET
VAYEFMSQAFSLYEDEISDSKAQLAAITLIIGTFERMKCFSEENHEPLRTQCALAASKLL
KKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVMECLKKALKIANQCMDPSLQVQLFI
EILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQINKHFHNTLEHLRLR

Sequence of entity 3 (C, F, I, L), FASTA

>5OSH_3 Interaptin (chains C, F, I, L)
MALEEYIRMAKNKEFFDALEEIAESAKNDETLRNELAKVLDDILKTDPSDPEAFRKIVAE
HQEFWDEHDPSLMEFNEGRFFGKSRKQYLKSDDFLNSTDPTYNFQKLHQFAAEQRVKLGL
EKSDTDTLVAILKNNPEECRAYIESKKPGLGNFSEGNVHGWLKEEYTPTIPPKAINKSTG
VLSDEAIKRIKEQARDLLLLKLINSSGNTQLLKDLRDAMSKPE

Primary citation

Molecular mechanism for the subversion of the retromer coat by the Legionella effector RidL. Romano-Moreno, M., Rojas, A.L., Williamson, C.D. et al. Proc Natl Acad Sci U S A (2017) 114:E11151-E11160. DOI 10.1073/pnas.1715361115 · PubMed

Other PDB entries of the same protein (UniProt Q9UBQ0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ESE 1.35 Å, Crystal structure of human Vps29 bound to a peptide from Vps35L
5GTU 1.5 Å, Structural and mechanistic insights into regulation of the retromer coat by TBC1d5
6XS7 1.58 Å, Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D2
6XSA 1.83 Å, Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L2
6XS5 2.01 Å, Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D1
1W24 2.1 Å, Crystal Structure Of human Vps29
8R0J 2.4 Å, Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl…
5WYH 2.46 Å, Crystal structure of RidL(1-200) complexed with VPS29
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)
6XS9 2.69 Å, Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L1
2R17 2.8 Å, Functional architecture of the retromer cargo-recognition complex

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