7U6F: Mouse retromer (VPS26/VPS35/VPS29) heterotrimers

Mouse retromer (VPS26/VPS35/VPS29) heterotrimers. Determined by electron microscopy at 4.9 Å resolution. Released 12 Oct 2022.

Method: Electron microscopy
Resolution: 4.9 Å
Organism: Mus musculus
Chains: 3
Atoms: 10,049
Mol. weight: 152.53 kDa
Released: 12 Oct 2022

Explore 7U6F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7U6F contains 49 α-helices and 34 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 B3: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	12-18	7	1
β-strand	29-30	2	2
α-helix	32-34	3
β-strand	36-37	2	2
β-strand	40-42	3	3
β-strand	46-56	11	1
β-strand	63-78	16	3
β-strand	86-101	16	3
β-strand	105-114	10	1
β-strand	122	1	3
β-strand	126-136	11	3
β-strand	143-151	9	3
β-strand	164-170	7	4
β-strand	174-180	7	4
β-strand	184-186	3	5
β-strand	190-200	11	4
β-strand	204-217	14	6
β-strand	224-237	14	6
β-strand	245-251	7	4
α-helix	252-255	4
β-strand	264	1	6
β-strand	268-280	13	6
β-strand	285-286	2	6
β-strand	289-292	4	6
β-strand	293-295	3	5

Chain B4: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	7
α-helix	22-25	4
β-strand	33-35	3	7
α-helix	43-52	10
β-strand	56-57	2	7
β-strand	73-77	5	8
β-strand	80-84	5	8
α-helix	96-106	11
β-strand	110-112	3	8
β-strand	120-124	5	8
β-strand	127-131	5	8
β-strand	149-155	7	7
β-strand	159-168	10	7
β-strand	171-180	10	7

Chain D1: 44 helices, 0 β-strands

Element	Residues	Length
α-helix	14-35	22
α-helix	39-50	12
α-helix	60-86	27
α-helix	94-97	4
α-helix	98-100	3
α-helix	104-121	18
α-helix	123-125	3
α-helix	126-136	11
α-helix	137-139	3
α-helix	143-156	14
α-helix	176-196	21
α-helix	203-205	3
α-helix	206-229	24
α-helix	235-237	3
α-helix	238-242	5
α-helix	243-251	9
α-helix	256-269	14
α-helix	273-275	3
α-helix	279-287	9
α-helix	295-310	16
α-helix	324-338	15
α-helix	344-360	17
α-helix	367-382	16
α-helix	393-408	16
α-helix	413-416	4
α-helix	421-424	4
α-helix	425-427	3
α-helix	430-446	17
α-helix	454-467	14
α-helix	485-497	13
α-helix	505-512	8
α-helix	513-517	5
α-helix	518-519	2
α-helix	525-545	21
α-helix	553-573	21
α-helix	579-594	16
α-helix	629-637	9
α-helix	646-658	13
α-helix	663-673	11
α-helix	674-677	4
α-helix	696-706	11
α-helix	713-731	19
α-helix	741-753	13
α-helix	763-777	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 35	D1	protein	796	Mus musculus	Q9EQH3 (AlphaFold model)
Vacuolar protein sorting-associated protein 26A	B3	protein	327	Mus musculus	P40336 (AlphaFold model)
Vacuolar protein sorting-associated protein 29	B4	protein	182	Mus musculus	Q9QZ88 (AlphaFold model)

Sequence of entity 1 (D1), FASTA

>7U6F_1 Vacuolar protein sorting-associated protein 35 (chains D1)
MPTTQQSPQDEQEKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELRTSMLSP
KSYYELYMAISDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVK
SFPQSRKDILKDLVEMCRGVQHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSM
DFVLLNFAEMNKLWVRMQHQGHSRDREKRERERQELRILVGTNLVRLSQLEGVNVERYKQ
IVLTGILEQVVNCRDALAQEYLMECIIQVFPDEFHLQTLNPFLRACAELHQNVNVKNIII
ALIDRLALFAHREDGPGIPAEIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLINLAMK
CYPDRVDYVDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKH
FHPLFEYFDYESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQDQPDQPVEDPD
PEDFADEQSLVGRFIHLLRSDDPDQQYLILNTARKHFGAGGNQRIRFTLPPLVFAAYQLA
FRYKENSQMDDKWEKKCQKIFSFAHQTISALIKAELAELPLRLFLQGALAAGEIGFENHE
TVAYEFMSQAFSLYEDEISDSKAQLAAITLIIGTFERMKCFSEENHEPLRTQCALAASKL
LKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVMECLKKALKIANQCMDPSLQVQLF
IEILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQINKHFHNTLEHLRSR
RESPESEGPIYEGLIL

Sequence of entity 2 (B3), FASTA

>7U6F_2 Vacuolar protein sorting-associated protein 26A (chains B3)
MSFLGGFFGPICEIDVALNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPG
KRLEHQGIRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYES
YIGANVRLRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEY
NKSKYHLKDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDGAP
VKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDEEDRRYFKQQEIILWRKAPE
KLRKQRTNFHQRFESPDSQASAEQPEM

Sequence of entity 3 (B4), FASTA

>7U6F_3 Vacuolar protein sorting-associated protein 29 (chains B4)
MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVR
GDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFE
AFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYK
KS

Primary citation

Improved mammalian retromer cryo-EM structures reveal a new assembly interface. Kendall, A.K., Chandra, M., Xie, B. et al. J Biol Chem (2022) 298:102523-102523. DOI 10.1016/j.jbc.2022.102523 · 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
6VAC 5.7 Å, Mouse retromer (VPS26/VPS35/VPS29) heterotrimer

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