9AU7: Human Retriever VPS35L/VPS29/VPS26C complex

Human Retriever VPS35L/VPS29/VPS26C complex bound to SNX17 peptide (Composite Map). Determined by electron microscopy at 3.4 Å resolution. Released 30 Oct 2024.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,601
Mol. weight: 167.84 kDa
Released: 30 Oct 2024

Explore 9AU7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9AU7 contains 50 α-helices and 36 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, 1 β-strand

Element	Residues	Length	Sheet
α-helix	117-127	11
α-helix	181-200	20
α-helix	204-215	12
α-helix	216-218	3
α-helix	227-252	26
α-helix	271-284	14
α-helix	290-298	9
α-helix	301-303	3
α-helix	304-307	4
α-helix	311-322	12
α-helix	323-325	3
β-strand	326	1	1
α-helix	329-346	18
α-helix	353-355	3
α-helix	356-365	10
α-helix	371-380	10
α-helix	384-387	4
α-helix	388-390	3
α-helix	392-403	12
α-helix	408-420	13
α-helix	425-434	10
α-helix	437-442	6
α-helix	444-453	10
α-helix	461-474	14
α-helix	479-481	3
α-helix	482-493	12
α-helix	499-516	18
α-helix	519-533	15
α-helix	535-541	7
α-helix	543-556	14
α-helix	560-565	6
α-helix	570-575	6
α-helix	579-595	17
α-helix	604-618	15
α-helix	627-641	15
α-helix	651-663	13
α-helix	668-687	20
α-helix	695-711	17
α-helix	712-714	3
α-helix	719-733	15
α-helix	743-751	9
α-helix	752-754	3
α-helix	769-783	15

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	2
α-helix	24-29	6
β-strand	37-40	4	2
α-helix	47-54	8
β-strand	59-62	4	2
β-strand	76-81	6	3
β-strand	84-89	6	3
α-helix	100-110	11
β-strand	114-116	3	3
β-strand	124-128	5	3
β-strand	131-135	5	3
β-strand	153-160	8	2
β-strand	163-172	10	2
β-strand	175-184	10	2

Chain C: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	4
β-strand	15-16	2	5
β-strand	21-30	10	4
β-strand	34-36	3	6
β-strand	38-47	10	7
β-strand	69-79	11	7
β-strand	82-84	3	6
β-strand	87-96	10	4
α-helix	105-107	3
β-strand	116-125	10	7
β-strand	133-136	4	7
β-strand	140-141	2	5
α-helix	143-145	3
β-strand	155-159	5	8
α-helix	161-163	3
α-helix	170-172	3
β-strand	176-182	7	8
β-strand	188	1	9
β-strand	193-202	10	8
β-strand	206-219	14	1
β-strand	221	1	10
β-strand	224	1	10
β-strand	227-239	13	1
α-helix	242-243	2
β-strand	247-252	6	8
β-strand	263-264	2	1
β-strand	268-280	13	1
β-strand	288-292	5	1
β-strand	295	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VPS35 endosomal protein-sorting factor-like	A	protein	963	Homo sapiens	Q7Z3J2 (AlphaFold model)
Vacuolar protein sorting-associated protein 29	B	protein	205	Homo sapiens	Q9UBQ0 (AlphaFold model)
Vacuolar protein sorting-associated protein 26C	C	protein	297	Homo sapiens	O14972 (AlphaFold model)
Sorting nexin-17	D	protein	20	Homo sapiens	Q15036 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9AU7_1 VPS35 endosomal protein-sorting factor-like (chains A)
MAVFPWHSRNRNYKAEFASCRLEAVPLEFGDYHPLKPITVTESKTKKVNRKGSTSSTSSS
SSSSVVDPLSSVLDGTDPLSMFAATADPAALAAAMDSSRRKRDRDDNSVVGSDFEPWTNK
RGEILARYTTTEKLSINLFMGSEKGKAGTATLAMSEKVRTRLEELDDFEEGSQKELLNLT
QQDYVNRIEELNQSLKDAWASDQKVKALKIVIQCSKLLSDTSVIQFYPSKFVLITDILDT
FGKLVYERIFSMCVDSRSVLPDHFSPENANDTAKETCLNWFFKIASIRELIPRFYVEASI
LKCNKFLSKTGISECLPRLTCMIRGIGDPLVSVYARAYLCRVGMEVAPHLKETLNKNFFD
FLLTFKQIHGDTVQNQLVVQGVELPSYLPLYPPAMDWIFQCISYHAPEALLTEMMERCKK
LGNNALLLNSVMSAFRAEFIATRSMDFIGMIKECDESGFPKHLLFRSLGLNLALADPPES
DRLQILNEAWKVITKLKNPQDYINCAEVWVEYTCKHFTKREVNTVLADVIKHMTPDRAFE
DSYPQLQLIIKKVIAHFHDFSVLFSVEKFLPFLDMFQKESVRVEVCKCIMDAFIKHQQEP
TKDPVILNALLHVCKTMHDSVNALTLEDEKRMLSYLINGFIKMVSFGRDFEQQLSFYVES
RSMFCNLEPVLVQLIHSVNRLAMETRKVMKGNHSRKTAAFVRACVAYCFITIPSLAGIFT
RLNLYLHSGQVALANQCLSQADAFFKAAISLVPEVPKMINIDGKMRPSESFLLEFLCNFF
STLLIVPDHPEHGVLFLVRELLNVIQDYTWEDNSDEKIRIYTCVLHLLSAMSQETYLYHI
DKVDSNDSLYGGDSKFLAENNKLCETVMAQILEHLKTLAKDEALKRQSSLGLSFFNSILA
HGDLRNNKLNQLSVNLWHLAQRHGCADTRTMVKTLEYIKKQSKQPDMTHLTELALRLPLQ
TRT

Sequence of entity 2 (B), FASTA

>9AU7_2 Vacuolar protein sorting-associated protein 29 (chains B)
MAGHRLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDV
HIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHT
HKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVER
IEYKKPENLYFQGGGSGGSHHHHHH

Sequence of entity 3 (C), FASTA

>9AU7_3 Vacuolar protein sorting-associated protein 26C (chains C)
MGTALDIKIKRANKVYHAGEVLSGVVVISSKDSVQHQGVSLTMEGTVNLQLSAKSVGVFE
AFYNSVKPIQIINSTIEMVKPGKFPSGKTEIPFEFPLHLKGNKVLYETYHGVFVNIQYTL
RCDMKRSLLAKDLTKTCEFIVHSAPQKGKFTPSPVDFTITPETLQNVKERALLPKFLLRG
HLNSTNCVITQPLTGELVVESSEAAIRSVELQLVRVETCGCAEGYARDATEIQNIQIADG
DVCRGLSVPIYMVFPRLFTCPTLETTNFKVEFEVNIVVLLHPDHLITENFPLKLCRI

Sequence of entity 4 (D), FASTA

>9AU7_4 Sorting nexin-17 (chains D)
ASASDVHGNFAFEGIGDEDL

Primary citation

Structural basis for Retriever-SNX17 assembly and endosomal sorting. Singla, A., Boesch, D.J., Fung, H.Y.J. et al. Nat Commun (2024) 15:10193-10193. DOI 10.1038/s41467-024-54583-6 · PubMed

Other PDB entries of the same protein (UniProt Q7Z3J2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ESE 1.35 Å, Crystal structure of human Vps29 bound to a peptide from Vps35L
8SYN 2.94 Å, Human VPS35L/VPS29/VPS26C Complex
8SYO 2.94 Å, Human Retriever VPS35L/VPS29/VPS26C Complex (Composite Map)
8SYM 3.2 Å, Human VPS29/VPS35L Complex (Locally refined map)
8P0V 6.5 Å, Structure of the human Commander complex coiled coils, DENND10 and partial Retriever…
8P0X 7.5 Å, Structure of the human Commander complex Retriever Subcomplex

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