5WYH: RidL(1-200)

Crystal structure of RidL(1-200) complexed with VPS29. Determined by X-ray diffraction at 2.46 Å resolution. Released 24 Jan 2018.

Method: X-ray diffraction
Resolution: 2.46 Å
Organisms: Homo sapiens, Legionella pneumophila subsp. pneumophila ATCC 43290
Chains: 4
Atoms: 6,379
Mol. weight: 87.51 kDa
Released: 24 Jan 2018

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

Secondary structure: helices and β-sheets

5WYH contains 26 α-helices and 31 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: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	1
β-strand	11	1	2
α-helix	20-25	6
β-strand	33-36	4	1
β-strand	41	1	2
α-helix	43-52	10
β-strand	55-58	4	1
β-strand	72-77	6	3
β-strand	80-85	6	3
α-helix	96-106	11
β-strand	110-113	4	3
β-strand	120-124	5	3
β-strand	127-131	5	3
β-strand	149-156	8	1
β-strand	159-168	10	1
β-strand	171-180	10	1

Chain B: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	12-26	15
α-helix	30-45	16
α-helix	51-60	10
α-helix	62-68	7
α-helix	85-89	5
α-helix	104-120	17
α-helix	125-133	9
α-helix	136-145	10
α-helix	161-164	4
β-strand	165-166	2	4
β-strand	174-175	2	4
α-helix	184-199	16

Chain C: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	5
β-strand	11	1	6
α-helix	20-25	6
β-strand	33-36	4	5
β-strand	41	1	6
α-helix	43-52	10
β-strand	55-58	4	5
β-strand	66	1	3
β-strand	72-77	6	7
β-strand	80-85	6	7
α-helix	96-106	11
β-strand	110-113	4	7
β-strand	120-124	5	7
β-strand	127-131	5	7
β-strand	149-156	8	5
β-strand	159-168	10	5
β-strand	171-180	10	5

Chain D: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	12-26	15
α-helix	30-45	16
α-helix	51-60	10
α-helix	62-68	7
α-helix	85-89	5
α-helix	104-120	17
α-helix	125-133	9
α-helix	136-145	10
α-helix	161-164	4
β-strand	165-166	2	8
β-strand	174-175	2	8
α-helix	184-198	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 29	A, C	protein	185	Homo sapiens	Q9UBQ0 (AlphaFold model)
Interaptin	B, D	protein	198	Legionella pneumophila subsp. pneumophila ATCC 43290	A0ABF7PFW6 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5WYH_1 Vacuolar protein sorting-associated protein 29 (chains A, C)
AGHRLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVH
IVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTH
KFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERI
EYKKP

Sequence of entity 2 (B, D), FASTA

>5WYH_2 Interaptin (chains B, D)
LEEYIRMAKNKEFFDALEEIAESAKNDETLRNELAKVLDDILKTDPSDPEAFRKIVAEHQ
EFWDEHDPSLMEFNEGRFFGKSRKQYLKSDDFLNSTDPTYNFQKLHQFAAEQRVKLGLEK
SDTDTLVAILKNNPEECRAYIESKKPGLGNFSEGNVHGWLKEEYTPTIPPKAINKSTGVL
SDEAIKRIKEQARDLLLL

Primary citation

Mechanism of inhibition of retromer transport by the bacterial effector RidL. Yao, J., Yang, F., Sun, X. et al. Proc Natl Acad Sci U S A (2018) 115:E1446-E1454. DOI 10.1073/pnas.1717383115 · 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…
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
8SYN 2.94 Å, Human VPS35L/VPS29/VPS26C Complex

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