8SYN: Human VPS35L/VPS29/VPS26C Complex

Human VPS35L/VPS29/VPS26C Complex. Determined by electron microscopy at 2.94 Å resolution. Released 1 Nov 2023.

Method: Electron microscopy
Resolution: 2.94 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,069
Mol. weight: 165.79 kDa
Released: 1 Nov 2023

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

Secondary structure: helices and β-sheets

8SYN contains 63 α-helices and 43 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: 54 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	1
α-helix	9-10	2
α-helix	13-20	8
β-strand	21	1	2
α-helix	22-23	2
β-strand	25-26	2	3
α-helix	115-116	2
α-helix	117-127	11
α-helix	133	1
β-strand	134	1	4
β-strand	179	1	4
α-helix	181-200	20
α-helix	204-217	14
α-helix	224-226	3
α-helix	227-253	27
α-helix	271-285	15
α-helix	290-299	10
α-helix	301-306	6
α-helix	311-322	12
α-helix	323-325	3
β-strand	326	1	5
α-helix	329-346	18
α-helix	351-364	14
α-helix	365-367	3
α-helix	371-380	10
α-helix	384-387	4
α-helix	388-390	3
α-helix	392-402	11
α-helix	408-419	12
α-helix	425-434	10
α-helix	437-442	6
α-helix	444-452	9
α-helix	461-472	12
α-helix	476-478	3
α-helix	479-481	3
α-helix	482-493	12
α-helix	499-516	18
α-helix	519-533	15
α-helix	538-541	4
α-helix	543-555	13
α-helix	560-563	4
α-helix	569-575	7
α-helix	579-595	17
β-strand	601	1	6
α-helix	604-618	15
α-helix	627-642	16
β-strand	644	1	6
α-helix	650-663	14
α-helix	668-688	21
α-helix	695-711	17
α-helix	712-714	3
α-helix	718-733	16
α-helix	739-751	13
α-helix	752-754	3
β-strand	758-761	4	7
β-strand	764-767	4	7
α-helix	769-783	15
α-helix	786-789	4
α-helix	796-807	12
α-helix	816-831	16
α-helix	846-849	4
α-helix	854-880	27
α-helix	884-900	17
β-strand	902	1	1
α-helix	907-922	16

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	3
α-helix	24-29	6
β-strand	37-40	4	3
α-helix	47-54	8
β-strand	59-62	4	3
β-strand	76-81	6	2
β-strand	84-89	6	2
α-helix	100-110	11
β-strand	114-117	4	2
β-strand	124-128	5	2
β-strand	131-135	5	2
β-strand	153-160	8	3
β-strand	163-172	10	3
β-strand	175-184	10	3

Chain C: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	8
β-strand	15-16	2	9
β-strand	21-28	8	8
β-strand	39-49	11	10
β-strand	69-79	11	10
β-strand	89-96	8	8
α-helix	106-108	3
β-strand	109-110	2	10
β-strand	114-124	11	10
β-strand	133-138	6	10
β-strand	140-141	2	9
α-helix	142-146	5
β-strand	155-159	5	11
α-helix	167-170	4
α-helix	174-175	2
β-strand	176-182	7	11
β-strand	188	1	12
α-helix	192	1
β-strand	193-202	10	11
β-strand	206-219	14	5
β-strand	226-239	14	5
β-strand	247-252	6	11
α-helix	253-255	3
β-strand	263-265	3	5
β-strand	268-280	13	5
β-strand	284-292	9	5
β-strand	295	1	12

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)

Sequence of entity 1 (A), FASTA

>8SYN_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

>8SYN_2 Vacuolar protein sorting-associated protein 29 (chains B)
MAGHRLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDV
HIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHT
HKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVER
IEYKKPENLYFQGGGSGGSHHHHHH

Sequence of entity 3 (C), FASTA

>8SYN_3 Vacuolar protein sorting-associated protein 26C (chains C)
MGTALDIKIKRANKVYHAGEVLSGVVVISSKDSVQHQGVSLTMEGTVNLQLSAKSVGVFE
AFYNSVKPIQIINSTIEMVKPGKFPSGKTEIPFEFPLHLKGNKVLYETYHGVFVNIQYTL
RCDMKRSLLAKDLTKTCEFIVHSAPQKGKFTPSPVDFTITPETLQNVKERALLPKFLLRG
HLNSTNCVITQPLTGELVVESSEAAIRSVELQLVRVETCGCAEGYARDATEIQNIQIADG
DVCRGLSVPIYMVFPRLFTCPTLETTNFKVEFEVNIVVLLHPDHLITENFPLKLCRI

Primary citation

Structural organization of the retriever-CCC endosomal recycling complex. Boesch, D.J., Singla, A., Han, Y. et al. Nat Struct Mol Biol (2024) 31:910-924. DOI 10.1038/s41594-023-01184-4 · 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
8SYO 2.94 Å, Human Retriever VPS35L/VPS29/VPS26C Complex (Composite Map)
8SYM 3.2 Å, Human VPS29/VPS35L Complex (Locally refined map)
9AU7 3.4 Å, Human Retriever VPS35L/VPS29/VPS26C complex bound to SNX17 peptide (Composite 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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