2R17: Vacuolar protein sorting-associated protein 29

Functional architecture of the retromer cargo-recognition complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 30 Oct 2007.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,640
Mol. weight: 110.92 kDa
Released: 30 Oct 2007

Explore 2R17 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2R17 contains 37 α-helices and 28 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	56-58	3	1
β-strand	72-77	6	3
β-strand	80-85	6	3
α-helix	96-106	11
β-strand	110-112	3	3
β-strand	120-124	5	3
β-strand	127-131	5	3
β-strand	149-155	7	1
β-strand	160-166	7	1
β-strand	173-179	7	1

Chain B: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	4
β-strand	11	1	5
α-helix	20-25	6
β-strand	33-36	4	4
β-strand	41	1	5
α-helix	43-52	10
β-strand	55-58	4	4
β-strand	72-77	6	6
β-strand	80-85	6	6
α-helix	96-106	11
β-strand	110-112	3	6
β-strand	120-124	5	6
β-strand	127-131	5	6
α-helix	146-148	3
β-strand	149-155	7	4
β-strand	159-168	10	4
β-strand	171-180	10	4

Chain C: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	488-498	11
α-helix	503-518	16
α-helix	525-544	20
α-helix	553-573	21
α-helix	578-594	17
α-helix	599-617	19
α-helix	621-635	15
α-helix	643-658	16
α-helix	663-672	10
α-helix	674-678	5
β-strand	681	1	7
β-strand	689	1	7
α-helix	693-709	17
α-helix	713-731	19
α-helix	740-751	12
α-helix	761-776	16

Chain D: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	485-497	13
α-helix	503-517	15
α-helix	525-528	4
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	621-637	17
α-helix	643-659	17
α-helix	663-673	11
α-helix	674-677	4
α-helix	696-708	13
α-helix	713-731	19
α-helix	742-753	12
α-helix	761-776	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 29	A, B	protein	183	Homo sapiens	Q9UBQ0 (AlphaFold model)
Vacuolar protein sorting-associated protein 35	C, D	protein	298	Homo sapiens	Q96QK1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2R17_1 Vacuolar protein sorting-associated protein 29 (chains A, B)
MMLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIV
RGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKF
EAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEY
KKP

Sequence of entity 2 (C, D), FASTA

>2R17_2 Vacuolar protein sorting-associated protein 35 (chains C, D)
DFADEQSLVGRFIHLLRSEDPDQQYLILNTARKHFGAGGNQRIRFTLPPLVFAAYQLAFR
YKENSKVDDKWEKKCQKIFSFAHQTISALIKAELAELPLRLFLQGALAAGEIGFENHETV
AYEFMSQAFSLYEDEISDSKAQLAAITLIIGTFERMKCFSEENHEPLRTQCALAASKLLK
KPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVMECLKKALKIANQCMDPSLQVQLFIE
ILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQINKHFHNTLEHLRLR

Primary citation

Functional architecture of the retromer cargo-recognition complex. Hierro, A., Rojas, A.L., Rojas, R. et al. Nature (2007) 449:1063-1067. DOI 10.1038/nature06216 · 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
8SYN 2.94 Å, Human VPS35L/VPS29/VPS26C Complex

Browse structure collections

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