8TTA: Retromer VPS29-VPS35

Structure of retromer VPS29-VPS35 (483-796) complexed with Fam21A repeat 21 (1328-1341). Determined by X-ray diffraction at 3.46 Å resolution. Released 21 Aug 2024.

Method: X-ray diffraction
Resolution: 3.46 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 7,948
Mol. weight: 118.88 kDa
Released: 21 Aug 2024

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

Secondary structure: helices and β-sheets

8TTA contains 36 α-helices and 32 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	7	1	2
α-helix	20-25	6
β-strand	33-36	4	1
α-helix	43-52	10
β-strand	55-57	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	134	1	2
β-strand	149-155	7	1
β-strand	159-168	10	1
β-strand	171-180	10	1

Chain B: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	488-498	11
α-helix	503-518	16
α-helix	524-526	3
α-helix	530-545	16
α-helix	553-573	21
α-helix	578-594	17
α-helix	599-616	18
α-helix	621-637	17
α-helix	643-658	16
α-helix	663-672	10
α-helix	674-678	5
β-strand	681	1	4
α-helix	683-685	3
β-strand	689	1	4
α-helix	693-707	15
α-helix	713-731	19
α-helix	740-752	13
α-helix	761-778	18

Chain C: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	5
β-strand	7	1	6
α-helix	20-25	6
β-strand	33-36	4	5
α-helix	43-52	10
β-strand	55-57	3	5
β-strand	72-77	6	7
β-strand	80-85	6	7
α-helix	96-106	11
β-strand	110-112	3	7
β-strand	120-124	5	7
β-strand	127-131	5	7
β-strand	134	1	6
β-strand	140	1	8
β-strand	143	1	8
β-strand	149-155	7	5
β-strand	160-168	9	5
β-strand	171-179	9	5

Chain D: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	503-518	16
α-helix	524-526	3
α-helix	530-545	16
α-helix	553-573	21
α-helix	579-594	16
α-helix	599-616	18
α-helix	621-637	17
α-helix	643-658	16
α-helix	663-672	10
α-helix	674-678	5
β-strand	681	1	9
β-strand	689	1	9
α-helix	693-707	15
α-helix	713-731	19
α-helix	740-752	13
α-helix	761-779	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 29	A, C	protein	192	Mus musculus	Q9QZ88 (AlphaFold model)
Vacuolar protein sorting-associated protein 35	B, D	protein	314	Mus musculus	Q9EQH3 (AlphaFold model)
Ser-asn-ile-phe-asp-asp-pro-leu-asn-ala-phe-gly-gly-gln	E, F	protein	14	Homo sapiens	Q641Q2 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8TTA_1 Vacuolar protein sorting-associated protein 29 (chains A, C)
GSPEFGTRDRMLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLK
TLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDI
LISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGD
DVKVERIEYKKS

Sequence of entity 2 (B, D), FASTA

>8TTA_2 Vacuolar protein sorting-associated protein 35 (chains B, D)
DFADEQSLVGRFIHLLRSDDPDQQYLILNTARKHFGAGGNQRIRFTLPPLVFAAYQLAFR
YKENSQMDDKWEKKCQKIFSFAHQTISALIKAELAELPLRLFLQGALAAGEIGFENHETV
AYEFMSQAFSLYEDEISDSKAQLAAITLIIGTFERMKCFSEENHEPLRTQCALAASKLLK
KPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVMECLKKALKIANQCMDPSLQVQLFIE
ILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQINKHFHNTLEHLRSRRE
SPESEGPIYEGLIL

Sequence of entity 3 (E, F), FASTA

>8TTA_3 SER-ASN-ILE-PHE-ASP-ASP-PRO-LEU-ASN-ALA-PHE-GLY-GLY-GLN (chains E, F)
SNIFDDPLNAFGGQ

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+
8TTC 3.01 Å, Structure of retromer VPS29-VPS35 (483-796) complexed with Fam21A repeat 20 (1289-1302)
3PSO 3.2 Å, Crystal structure of mouse VPS29 complexed with Zn2+
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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