6VAC: Mouse retromer (VPS26/VPS35/VPS29) heterotrimer

Mouse retromer (VPS26/VPS35/VPS29) heterotrimer. Determined by electron microscopy at 5.7 Å resolution. Released 19 Feb 2020.

Method: Electron microscopy
Resolution: 5.7 Å
Organism: Mus musculus
Chains: 3
Atoms: 5,957
Mol. weight: 150.51 kDa
Released: 19 Feb 2020

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

Secondary structure: helices and β-sheets

6VAC contains 47 α-helices and 46 β-strands across 3 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: 42 helices, 0 β-strands

Element	Residues	Length
α-helix	17-35	19
α-helix	39-50	12
α-helix	51-54	4
α-helix	60-86	27
α-helix	94-97	4
α-helix	104-120	17
α-helix	123-125	3
α-helix	126-136	11
α-helix	137-139	3
α-helix	143-156	14
α-helix	176-198	23
α-helix	206-213	8
α-helix	217-228	12
α-helix	235-237	3
α-helix	238-243	6
α-helix	244-251	8
α-helix	256-269	14
α-helix	272-274	3
α-helix	279-287	9
α-helix	296-302	7
α-helix	304-311	8
α-helix	324-338	15
α-helix	345-361	17
α-helix	366-382	17
α-helix	393-408	16
α-helix	413-416	4
α-helix	421-424	4
α-helix	430-446	17
α-helix	454-468	15
α-helix	485-497	13
α-helix	503-520	18
α-helix	525-543	19
α-helix	553-573	21
α-helix	578-594	17
α-helix	600-616	17
α-helix	621-636	16
α-helix	643-659	17
α-helix	663-675	13
α-helix	697-707	11
α-helix	713-731	19
α-helix	741-753	13
α-helix	763-776	14

Chain B: 2 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	12-18	7	1
β-strand	42	1	2
β-strand	49-56	8	1
β-strand	63-64	2	3
β-strand	68-78	11	4
α-helix	82-84	3
β-strand	86-89	4	4
β-strand	92-96	5	4
β-strand	100-101	2	3
β-strand	106-110	5	1
β-strand	122	1	4
β-strand	126-136	11	4
β-strand	143-149	7	4
β-strand	151	1	2
β-strand	154	1	5
β-strand	164-166	3	6
β-strand	169-170	2	7
β-strand	174-175	2	7
β-strand	178-180	3	6
β-strand	184-186	3	8
β-strand	190-196	7	6
β-strand	199-200	2	7
β-strand	204	1	9
β-strand	209-219	11	10
β-strand	222-224	3	10
β-strand	231-232	2	10
β-strand	245-251	7	6
β-strand	264	1	10
β-strand	268-276	9	10
β-strand	278-279	2	11
β-strand	280	1	9
β-strand	285-286	2	11
β-strand	289-292	4	10
β-strand	293-295	3	8
β-strand	296	1	5
α-helix	297-298	2

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
α-helix	20-25	6
β-strand	33-36	4	12
α-helix	43-52	10
β-strand	55-58	4	12
β-strand	72-77	6	13
β-strand	80-85	6	13
α-helix	98-106	9
β-strand	110-112	3	13
β-strand	120-124	5	13
β-strand	127-131	5	13
β-strand	149-151	3	12
β-strand	155	1	12
β-strand	159-168	10	12
β-strand	171-180	10	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 35	A	protein	796	Mus musculus	Q9EQH3 (AlphaFold model)
Vacuolar protein sorting-associated protein 26A	B	protein	327	Mus musculus	P40336 (AlphaFold model)
Vacuolar protein sorting-associated protein 29	C	protein	182	Mus musculus	Q9QZ88 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6VAC_1 Vacuolar protein sorting-associated protein 35 (chains A)
MPTTQQSPQDEQEKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELRTSMLSP
KSYYELYMAISDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVK
SFPQSRKDILKDLVEMCRGVQHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSM
DFVLLNFAEMNKLWVRMQHQGHSRDREKRERERQELRILVGTNLVRLSQLEGVNVERYKQ
IVLTGILEQVVNCRDALAQEYLMECIIQVFPDEFHLQTLNPFLRACAELHQNVNVKNIII
ALIDRLALFAHREDGPGIPAEIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLINLAMK
CYPDRVDYVDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKH
FHPLFEYFDYESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQDQPDQPVEDPD
PEDFADEQSLVGRFIHLLRSDDPDQQYLILNTARKHFGAGGNQRIRFTLPPLVFAAYQLA
FRYKENSQMDDKWEKKCQKIFSFAHQTISALIKAELAELPLRLFLQGALAAGEIGFENHE
TVAYEFMSQAFSLYEDEISDSKAQLAAITLIIGTFERMKCFSEENHEPLRTQCALAASKL
LKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVMECLKKALKIANQCMDPSLQVQLF
IEILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQINKHFHNTLEHLRSR
RESPESEGPIYEGLIL

Sequence of entity 2 (B), FASTA

>6VAC_2 Vacuolar protein sorting-associated protein 26A (chains B)
MSFLGGFFGPICEIDVALNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPG
KRLEHQGIRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYES
YIGANVRLRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEY
NKSKYHLKDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDGAP
VKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDEEDRRYFKQQEIILWRKAPE
KLRKQRTNFHQRFESPDSQASAEQPEM

Sequence of entity 3 (C), FASTA

>6VAC_3 Vacuolar protein sorting-associated protein 29 (chains C)
MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVR
GDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFE
AFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYK
KS

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 Q9EQH3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8TTC 3.01 Å, Structure of retromer VPS29-VPS35 (483-796) complexed with Fam21A repeat 20 (1289-1302)
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

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