6VAB: Vacuolar protein sorting-associated protein 29

Mouse retromer sub-structure: VPS35/VPS35 flat dimer. Determined by electron microscopy at 4.9 Å resolution. Released 19 Feb 2020.

Method: Electron microscopy
Resolution: 4.9 Å
Organism: Mus musculus
Chains: 4
Atoms: 4,642
Mol. weight: 224.69 kDa
Released: 19 Feb 2020

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

Secondary structure: helices and β-sheets

6VAB contains 34 α-helices and 26 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.

Chains A and C: 3 helices, 12 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	44-50	7
β-strand	55-58	4	1
β-strand	74-77	4	2
β-strand	80-84	5	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	149-155	7	1
β-strand	159-168	10	1
β-strand	171-175	5	1
β-strand	179-180	2	1

Chain B: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	485-496	12
α-helix	503-512	10
α-helix	513-517	5
α-helix	524-545	22
α-helix	553-572	20
α-helix	578-594	17
α-helix	599-613	15
α-helix	621-637	17
α-helix	647-658	12
α-helix	663-675	13
α-helix	697-707	11
α-helix	713-732	20
α-helix	742-750	9
α-helix	763-777	15

Chain D: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	484-487	4
α-helix	489-499	11
α-helix	503-516	14
α-helix	524-545	22
α-helix	553-572	20
α-helix	579-594	16
α-helix	599-613	15
α-helix	621-636	16
α-helix	643-658	16
α-helix	663-678	16
β-strand	681	1	5
β-strand	689	1	5
α-helix	696-706	11
α-helix	713-729	17
α-helix	743-749	7
α-helix	761-776	16

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	796	Mus musculus	Q9EQH3 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6VAB_1 Vacuolar protein sorting-associated protein 29 (chains A, C)
MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVR
GDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFE
AFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYK
KS

Sequence of entity 2 (B, D), FASTA

>6VAB_2 Vacuolar protein sorting-associated protein 35 (chains B, D)
MPTTQQSPQDEQEKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELRTSMLSP
KSYYELYMAISDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVK
SFPQSRKDILKDLVEMCRGVQHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSM
DFVLLNFAEMNKLWVRMQHQGHSRDREKRERERQELRILVGTNLVRLSQLEGVNVERYKQ
IVLTGILEQVVNCRDALAQEYLMECIIQVFPDEFHLQTLNPFLRACAELHQNVNVKNIII
ALIDRLALFAHREDGPGIPAEIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLINLAMK
CYPDRVDYVDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKH
FHPLFEYFDYESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQDQPDQPVEDPD
PEDFADEQSLVGRFIHLLRSDDPDQQYLILNTARKHFGAGGNQRIRFTLPPLVFAAYQLA
FRYKENSQMDDKWEKKCQKIFSFAHQTISALIKAELAELPLRLFLQGALAAGEIGFENHE
TVAYEFMSQAFSLYEDEISDSKAQLAAITLIIGTFERMKCFSEENHEPLRTQCALAASKL
LKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVMECLKKALKIANQCMDPSLQVQLF
IEILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQINKHFHNTLEHLRSR
RESPESEGPIYEGLIL

Primary citation

Mammalian Retromer Is an Adaptable Scaffold for Cargo Sorting from Endosomes. Kendall, A.K., Xie, B., Xu, P. et al. Structure (2020) 28:393-405.e4. DOI 10.1016/j.str.2020.01.009 · 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+
8TTA 3.46 Å, Structure of retromer VPS29-VPS35 (483-796) complexed with Fam21A repeat 21 (1328-1341)
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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