9Q8M: VPS35-VPS26-SNX12 Complex

VPS35-VPS26-SNX12 Complex. Determined by X-ray diffraction at 3.13 Å resolution. Released 9 Sept 2026.

Method: X-ray diffraction
Resolution: 3.13 Å
Organisms: Homo sapiens, Human papillomavirus 16
Chains: 4
Atoms: 7,504
Mol. weight: 107.28 kDa
Released: 9 Sept 2026

Explore 9Q8M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q8M contains 49 α-helices and 34 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.

Chain A: 33 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	12-35	24
α-helix	39-50	12
α-helix	51-54	4
α-helix	60-86	27
α-helix	90-91	2
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
β-strand	140	1	1
α-helix	143-156	14
α-helix	176-196	21
α-helix	197-199	3
α-helix	203-205	3
α-helix	206-215	10
α-helix	217-228	12
α-helix	235-237	3
α-helix	238-242	5
α-helix	243-252	10
α-helix	256-269	14
α-helix	272-276	5
α-helix	279-287	9
α-helix	295-311	17
α-helix	324-338	15
α-helix	344-361	18
α-helix	366-382	17
α-helix	385-387	3
α-helix	393-408	16
α-helix	413-416	4
α-helix	423-427	5
α-helix	430-446	17
α-helix	454-468	15

Chain B: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	12-18	7	2
β-strand	26-30	5	3
α-helix	32-34	3
β-strand	36-40	5	3
β-strand	41-42	2	4
β-strand	48-56	9	2
β-strand	59	1	5
β-strand	61	1	5
β-strand	63-65	3	6
β-strand	68-78	11	7
β-strand	81-96	16	7
β-strand	99-101	3	6
β-strand	105-111	7	2
β-strand	121-122	2	7
β-strand	126-136	11	7
β-strand	143-149	7	7
β-strand	150-151	2	4
β-strand	155	1	8
α-helix	162-163	2
β-strand	164-168	5	9
β-strand	174-180	7	9
β-strand	184-186	3	10
β-strand	190-200	11	9
β-strand	204-219	16	1
β-strand	222-237	16	1
β-strand	245-251	7	9
α-helix	252-255	4
α-helix	257-260	4
β-strand	261-264	4	1
β-strand	268-280	13	1
β-strand	285-292	8	1
β-strand	293-295	3	10
α-helix	296	1
β-strand	297	1	8
α-helix	298-299	2

Chain C: 10 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
α-helix	19-23	5
α-helix	25-26	2
β-strand	30-39	10	11
β-strand	48-56	9	11
β-strand	65-71	7	11
α-helix	72-85	14
α-helix	90-93	4
α-helix	99-101	3
α-helix	109-111	3
α-helix	113-132	20
α-helix	134-136	3
α-helix	140-146	7

Chain E: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	452-454	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 35	A	protein	459	Homo sapiens	Q96QK1 (AlphaFold model)
Vacuolar protein sorting-associated protein 26A	B	protein	293	Homo sapiens	O75436 (AlphaFold model)
Sorting nexin-12	C	protein	150	Homo sapiens	Q9UMY4 (AlphaFold model)
Minor capsid protein L2	E	protein	8	Human papillomavirus 16	P03107 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9Q8M_1 Vacuolar protein sorting-associated protein 35 (chains A)
EQEKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELRTSMLSPKSYYELYMAI
SDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVKSFPQSRKDIL
KDLVEMCRGVQHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFAEM
NKLWVRMQHQGHSRDREKRERERQELRILVGTNLVRLSQLEGVNVERYKQIVLTGILEQV
VNCRDALAQEYLMECIIQVFPDEFHLQTLNPFLRACAELHQNVNVKNIIIALIDRLALFA
HREDGPGIPADIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLINLAMKCYPDRVDYVD
KVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKHFHPLFEYFDY
ESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQ

Sequence of entity 2 (B), FASTA

>9Q8M_2 Vacuolar protein sorting-associated protein 26A (chains B)
FGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQG
IRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVR
LRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHL
KDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIP
IRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDEEDRRYFKQQEIILWRKAPE

Sequence of entity 3 (C), FASTA

>9Q8M_3 Sorting nexin-12 (chains C)
DTAVADTRRLNSKPQNLTDAYGPPSNFLEIDIFNPQTVGVGRARFTTYEVRMRTNLPIFK
LKESCVRRRYSDFEWLKNELERDSKIVVPPLPGKALKRQLPFRGDEGIFEESFIEERRQG
LEQFINKIAGHPLAQNERCLHMFLQEEAID

Sequence of entity 4 (E), FASTA

>9Q8M_4 Minor capsid protein L2 (chains E)
SYYMLRKR

Primary citation

VPS35-VPS26-SNX12 Complex. Pardo, M., Rojas, A.L., Hierro, A. To be published.

Other PDB entries of the same protein (UniProt Q96QK1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8R0J 2.4 Å, Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl…
8R02 2.5 Å, Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl…
5OSI 2.52 Å, Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176)
5F0J 2.7 Å, Structure of retromer VPS26-VPS35 subunits bound to SNX3
5F0P 2.78 Å, Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled)
2R17 2.8 Å, Functional architecture of the retromer cargo-recognition complex
5F0K 3.07 Å, Structure of VPS35 N terminal region
5F0M 3.1 Å, Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled)
8RKS 3.1 Å, Structure of VPS29-VPS35 bound to the LFa motif R21 of Fam21.
5F0L 3.2 Å, Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1
5OSH 4.3 Å, Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236)
7BLN 8.9 Å, VPS35/VPS29 arch of metazoan membrane-assembled retromer:SNX3 complex modelled with…

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