5OSI: Retromer VPS29-VPS35C subunits

Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176). Determined by X-ray diffraction at 2.52 Å resolution. Released 13 Dec 2017.

Method: X-ray diffraction
Resolution: 2.52 Å
Organisms: Homo sapiens, Legionella pneumophila subsp. pneumophila ATCC 43290
Chains: 11
Atoms: 15,918
Mol. weight: 231.05 kDa
Released: 13 Dec 2017

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

Secondary structure: helices and β-sheets

5OSI contains 75 α-helices and 59 β-strands across 9 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: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	20-25	6
β-strand	33-36	4	1
α-helix	43-50	8
β-strand	55-58	4	1
β-strand	72-77	6	2
β-strand	80-85	6	2
α-helix	96-106	11
β-strand	110-112	3	2
β-strand	120-124	5	2
β-strand	127-131	5	2
β-strand	140	1	3
β-strand	143	1	3
α-helix	146-148	3
β-strand	149-156	8	1
β-strand	159-168	10	1
β-strand	171-180	10	1

Chain B: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	485-498	14
α-helix	503-518	16
α-helix	521-528	8
α-helix	530-545	16
α-helix	553-573	21
α-helix	578-594	17
α-helix	599-617	19
α-helix	621-637	17
α-helix	643-657	15
α-helix	663-672	10
α-helix	674-678	5
β-strand	681	1	4
β-strand	689	1	4
α-helix	693-708	16
α-helix	713-732	20
α-helix	740-753	14
α-helix	754-756	3
α-helix	761-778	18

Chain C: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	166	1	5
β-strand	174	1	5

Chain D: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
α-helix	20-25	6
β-strand	33-36	4	6
α-helix	43-52	10
β-strand	55-58	4	6
β-strand	72-77	6	7
β-strand	80-85	6	7
α-helix	96-106	11
β-strand	110-112	3	7
β-strand	120-124	5	7
β-strand	127-131	5	7
β-strand	149-155	7	6
β-strand	160-168	9	6
β-strand	171-176	6	6
α-helix	177-178	2
β-strand	180	1	7

Chain E: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	487-500	14
α-helix	503-517	15
α-helix	524-528	5
α-helix	530-545	16
α-helix	553-573	21
α-helix	578-594	17
α-helix	599-616	18
α-helix	621-637	17
β-strand	641	1	8
α-helix	643-658	16
α-helix	663-678	16
β-strand	682	1	8
α-helix	693-708	16
α-helix	713-732	20
α-helix	740-753	14
α-helix	761-778	18

Chain G: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	9
β-strand	11	1	10
α-helix	20-25	6
β-strand	33-36	4	9
β-strand	41	1	10
α-helix	43-52	10
β-strand	55-58	4	9
β-strand	72-77	6	11
β-strand	80-85	6	11
α-helix	96-106	11
β-strand	110-112	3	11
β-strand	120-124	5	11
β-strand	127-131	5	11
β-strand	149-155	7	9
β-strand	159-168	10	9
β-strand	171-180	10	9

Chain H: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	491-497	7
α-helix	503-517	15
α-helix	518-520	3
α-helix	525-528	4
α-helix	530-545	16
α-helix	553-573	21
α-helix	578-594	17
α-helix	599-617	19
α-helix	621-636	16
α-helix	643-658	16
α-helix	663-678	16
α-helix	693-708	16
α-helix	713-731	19
α-helix	740-753	14
α-helix	758-759	2
α-helix	761-778	18

Chain J: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	12
β-strand	11	1	13
α-helix	20-25	6
β-strand	33-36	4	12
β-strand	41	1	13
α-helix	43-52	10
β-strand	55-58	4	12
β-strand	72-77	6	14
β-strand	80-85	6	14
α-helix	96-106	11
β-strand	110-112	3	14
β-strand	120-124	5	14
β-strand	127-131	5	14
β-strand	149-156	8	12
β-strand	159-168	10	12
β-strand	171-180	10	12

1 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	311	Homo sapiens	Q96QK1 (AlphaFold model)
Interaptin	C, F, I	protein	14	Legionella pneumophila subsp. pneumophila ATCC 43290	Q5ZT54 (AlphaFold model)

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

>5OSI_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

>5OSI_2 Vacuolar protein sorting-associated protein 35 (chains B, E, H, K)
QPDQPVEDPDPEDFADEQSLVGRFIHLLRSEDPDQQYLILNTARKHFGAGGNQRIRFTLP
PLVFAAYQLAFRYKENSKVDDKWEKKCQKIFSFAHQTISALIKAELAELPLRLFLQGALA
AGEIGFENHETVAYEFMSQAFSLYEDEISDSKAQLAAITLIIGTFERMKCFSEENHEPLR
TQCALAASKLLKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVMECLKKALKIANQC
MDPSLQVQLFIEILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQINKHF
HNTLEHLRLRR

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

>5OSI_3 Interaptin (chains C, F, I)
KEEYTPTIPPKAIN

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…
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
8SYN 2.94 Å, Human VPS35L/VPS29/VPS26C Complex

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