6XS9: Human Vps29

Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L1. Determined by X-ray diffraction at 2.69 Å resolution. Released 21 Jul 2021.

Method: X-ray diffraction
Resolution: 2.69 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 3,562
Mol. weight: 51.18 kDa
Ligands: O4B, MLI
Released: 21 Jul 2021

Explore 6XS9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XS9 contains 8 α-helices and 37 β-strands across 6 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, 14 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
β-strand	90	1	4
α-helix	96-106	11
β-strand	110-112	3	3
β-strand	120-124	5	3
β-strand	127-131	5	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: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	5
α-helix	20-25	6
β-strand	33-36	4	5
α-helix	44-52	9
β-strand	55-58	4	5
β-strand	72-77	6	6
β-strand	80-85	6	6
α-helix	96-106	11
β-strand	110-113	4	6
β-strand	119-124	6	6
β-strand	127-132	6	6
β-strand	134	1	7
α-helix	146-147	2
β-strand	148	1	7
β-strand	149-156	8	5
β-strand	159-168	10	5
β-strand	171-180	10	5

Chains C and D: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	8
β-strand	9	1	8
β-strand	11	1	1

Chains E and F: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	10
β-strand	7-9	3	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 29	A	protein	192	Homo sapiens	Q9UBQ0 (AlphaFold model)
Vacuolar protein sorting-associated protein 29	B	protein	192	Homo sapiens	Q9UBQ0 (AlphaFold model)
48V-tyr-ile-lys-thr-pro-leu-gly-thr-phe-pro-asn-arg-his-gly	C, D, E, F	protein	15	synthetic construct

Sequence of entity 1 (A), FASTA

>6XS9_1 Vacuolar protein sorting-associated protein 29 (chains A)
GSPEFGTRDRMLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLK
TLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDI
LISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGD
DVKVERIEYKKP

Sequence of entity 2 (B), FASTA

>6XS9_2 Vacuolar protein sorting-associated protein 29 (chains B)
GSPEFGTRDRMLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLK
TLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDI
LISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGD
DVKVERIEYKKP

Sequence of entity 3 (C, D, E, F), FASTA

>6XS9_3 48V-TYR-ILE-LYS-THR-PRO-LEU-GLY-THR-PHE-PRO-ASN-ARG-HIS-GLY (chains C, D, E, F)
XYIKTPLGTFPNRHG

Ligands and cofactors

ID	Name	Formula	Copies
O4B	1,4,7,10,13,16-hexaoxacyclooctadecane	C12 H24 O6	1
MLI	Malonate ion	C3 H2 O4	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

De novo macrocyclic peptides for inhibiting, stabilizing, and probing the function of the retromer endosomal trafficking complex. Chen, K.E., Guo, Q., Hill, T.A. et al. Sci Adv (2021) 7:eabg4007-eabg4007. DOI 10.1126/sciadv.abg4007 · 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)
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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