8R02: Vacuolar protein sorting-associated protein 29

Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl guanylhydrazone, 2a. Determined by X-ray diffraction at 2.5 Å resolution. Released 27 Mar 2024.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,814
Mol. weight: 112.59 kDa
Ligands: XFZ
Released: 27 Mar 2024

Explore 8R02 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R02 contains 41 α-helices and 30 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, 11 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	43-52	10
β-strand	56-58	3	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	149-154	6	1
β-strand	159-168	10	1
β-strand	171-180	10	1

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
α-helix	20-25	6
β-strand	33-36	4	3
α-helix	43-52	10
β-strand	56-58	3	3
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	120-124	5	4
β-strand	127-131	5	4
β-strand	149-155	7	3
β-strand	159-168	10	3
β-strand	171-180	10	3

Chain C: 18 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	479-480	2
α-helix	481-483	3
α-helix	485-498	14
α-helix	503-518	16
α-helix	522-528	7
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
β-strand	641	1	5
α-helix	643-658	16
α-helix	663-678	16
β-strand	681	1	6
β-strand	682	1	5
β-strand	689	1	6
α-helix	693-708	16
α-helix	713-732	20
α-helix	740-753	14
α-helix	754-756	3
α-helix	758-759	2
α-helix	761-778	18

Chain D: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	491-497	7
α-helix	503-518	16
α-helix	522-528	7
α-helix	530-545	16
α-helix	546-548	3
α-helix	553-573	21
α-helix	578-594	17
α-helix	599-617	19
α-helix	621-636	16
β-strand	641	1	7
α-helix	643-658	16
α-helix	663-678	16
β-strand	681	1	8
β-strand	682	1	7
β-strand	689	1	8
α-helix	693-708	16
α-helix	713-732	20
α-helix	740-753	14
α-helix	754-756	3
α-helix	758-759	2
α-helix	761-777	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 29	A, B	protein	185	Homo sapiens	Q9UBQ0 (AlphaFold model)
Vacuolar protein sorting-associated protein 35	C, D	protein	306	Homo sapiens	Q96QK1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8R02_1 Vacuolar protein sorting-associated protein 29 (chains A, B)
MEHMLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVH
IVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTH
KFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERI
EYKKP

Sequence of entity 2 (C, D), FASTA

>8R02_2 Vacuolar protein sorting-associated protein 35 (chains C, D)
MVEDPDPEDFADEQSLVGRFIHLLRSEDPDQQYLILNTARKHFGAGGNQRIRFTLPPLVF
AAYQLAFRYKENSKVDDKWEKKCQKIFSFAHQTISALIKAELAELPLRLFLQGALAAGEI
GFENHETVAYEFMSQAFSLYEDEISDSKAQLAAITLIIGTFERMKCFSEENHEPLRTQCA
LAASKLLKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVMECLKKALKIANQCMDPS
LQVQLFIEILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQINKHFHNTL
EHLRLR

Ligands and cofactors

ID	Name	Formula	Copies
XFZ	Bis-1,3-phenyl guanylhydrazon	C10 H14 N8	1

Primary citation

Stabilization of the retromer complex: Analysis of novel binding sites of bis-1,3-phenyl guanylhydrazone 2a to the VPS29/VPS35 interface. Fagnani, E., Boni, F., Seneci, P. et al. Comput Struct Biotechnol J (2024) 23:1088-1093. DOI 10.1016/j.csbj.2024.02.026 · 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
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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