8TTC: Retromer VPS29-VPS35

Structure of retromer VPS29-VPS35 (483-796) complexed with Fam21A repeat 20 (1289-1302). Determined by X-ray diffraction at 3.01 Å resolution. Released 21 Aug 2024.

Method: X-ray diffraction
Resolution: 3.01 Å
Organisms: Mus musculus, Homo sapiens
Chains: 5
Atoms: 7,807
Mol. weight: 115.72 kDa
Ligands: CIT
Released: 21 Aug 2024

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

Secondary structure: helices and β-sheets

8TTC contains 36 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, 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	43-52	10
β-strand	55-58	4	1
β-strand	72-77	6	2
β-strand	79-85	7	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
β-strand	149-155	7	1
β-strand	159-168	10	1
β-strand	171-180	10	1

Chain B: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	503-518	16
α-helix	521-545	25
α-helix	553-573	21
α-helix	578-594	17
α-helix	599-617	19
α-helix	621-637	17
α-helix	643-658	16
α-helix	663-673	11
α-helix	676-679	4
β-strand	681	1	4
α-helix	683-685	3
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: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	5
α-helix	20-25	6
β-strand	33-36	4	5
α-helix	43-52	10
β-strand	56-58	3	5
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
β-strand	140	1	7
β-strand	143	1	7
β-strand	149-155	7	5
β-strand	159-168	10	5
β-strand	171-180	10	5

Chain D: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	497-499	3
α-helix	503-518	16
α-helix	525-545	21
α-helix	553-572	20
α-helix	578-594	17
α-helix	599-617	19
α-helix	621-637	17
α-helix	643-658	16
α-helix	663-672	10
α-helix	674-678	5
β-strand	681	1	8
α-helix	683-685	3
β-strand	689	1	8
α-helix	693-708	16
α-helix	713-731	19
α-helix	740-753	14
α-helix	761-778	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 29	A, C	protein	182	Mus musculus	Q9QZ88 (AlphaFold model)
Vacuolar protein sorting-associated protein 35	B, D	protein	316	Mus musculus	Q9EQH3 (AlphaFold model)
Ser-ile-phe-asp-asp-asp-met-asp-asp-ile-phe-ser-ser-gly	E	protein	14	Homo sapiens	Q641Q2 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8TTC_1 Vacuolar protein sorting-associated protein 29 (chains A, C)
MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVR
GDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFE
AFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYK
KS

Sequence of entity 2 (B, D), FASTA

>8TTC_2 Vacuolar protein sorting-associated protein 35 (chains B, D)
GSDFADEQSLVGRFIHLLRSDDPDQQYLILNTARKHFGAGGNQRIRFTLPPLVFAAYQLA
FRYKENSQMDDKWEKKCQKIFSFAHQTISALIKAELAELPLRLFLQGALAAGEIGFENHE
TVAYEFMSQAFSLYEDEISDSKAQLAAITLIIGTFERMKCFSEENHEPLRTQCALAASKL
LKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVMECLKKALKIANQCMDPSLQVQLF
IEILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQINKHFHNTLEHLRSR
RESPESEGPIYEGLIL

Sequence of entity 3 (E), FASTA

>8TTC_3 SER-ILE-PHE-ASP-ASP-ASP-MET-ASP-ASP-ILE-PHE-SER-SER-GLY (chains E)
SIFDDDMDDIFSSG

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	2

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

Primary citation

Structural basis for coupling of the WASH subunit FAM21 with the endosomal SNX27-Retromer complex. Guo, Q., Chen, K.E., Gimenez-Andres, M. et al. Proc Natl Acad Sci U S A (2024) 121:e2405041121-e2405041121. DOI 10.1073/pnas.2405041121 · PubMed

Other PDB entries of the same protein (UniProt Q9QZ88 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8FUD 1.68 Å, Crystal structure of Vps29 in complex with Chaetomium thermophilum Vps5 (71 to 80)
1Z2W 2.0 Å, Crystal structure of mouse Vps29 complexed with Mn2+
8TTD 2.01 Å, Structure of VPS29 complexed with Fam21A repeat 21 (1328-1341)
1Z2X 2.22 Å, Crystal structure of mouse Vps29
9O9I 2.35 Å, Crystal structure of mouse Vps29 bound to DENND4C peptide (re-refinement)
3PSN 2.4 Å, Crystal structure of mouse VPS29 complexed with Mn2+
3PSO 3.2 Å, Crystal structure of mouse VPS29 complexed with Zn2+
8TTA 3.46 Å, Structure of retromer VPS29-VPS35 (483-796) complexed with Fam21A repeat 21 (1328-1341)
6VAB 4.9 Å, Mouse retromer sub-structure: VPS35/VPS35 flat dimer
7U6F 4.9 Å, Mouse retromer (VPS26/VPS35/VPS29) heterotrimers
6VAC 5.7 Å, Mouse retromer (VPS26/VPS35/VPS29) heterotrimer
6TL0 Solution structure and 1H, 13C and 15N chemical shift assignments for the complex of…

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