7BLO: Vacuolar protein sorting-associated protein 26A

VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 complex modelled with human proteins. Determined by electron microscopy at 9.5 Å resolution. Released 3 Mar 2021.

Method: Electron microscopy
Resolution: 9.5 Å
Organisms: Homo sapiens, Mus musculus
Chains: 8
Atoms: 13,288
Mol. weight: 189.67 kDa
Ligands: PIB
Released: 3 Mar 2021

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

Secondary structure: helices and β-sheets

7BLO contains 79 α-helices and 63 β-strands across 8 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: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	14-35	22
α-helix	39-52	14
α-helix	60-86	27
α-helix	94-98	5
α-helix	104-121	18
α-helix	123-125	3
α-helix	126-136	11
α-helix	137-139	3
α-helix	143-160	18
α-helix	176-199	24
α-helix	203-205	3
α-helix	206-229	24
α-helix	235-237	3
α-helix	238-242	5
α-helix	243-252	10
α-helix	257-269	13
α-helix	272-287	16
α-helix	296-310	15
α-helix	324-338	15
α-helix	344-361	18

Chain C: 21 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	14-35	22
α-helix	39-52	14
α-helix	60-86	27
α-helix	94-98	5
α-helix	104-121	18
α-helix	123-125	3
α-helix	126-136	11
α-helix	137-139	3
β-strand	140	1	15
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	243-253	11
α-helix	257-269	13
α-helix	272-277	6
α-helix	279-287	9
α-helix	295-310	16
α-helix	324-338	15
α-helix	344-361	18

Chains F and J: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	12-18	7	9
β-strand	26-30	5	10
α-helix	32-34	3
β-strand	36-42	7	10
β-strand	48-56	9	9
β-strand	63-65	3	11
β-strand	68-78	11	10
α-helix	82-84	3
β-strand	85-96	12	10
β-strand	99-101	3	11
β-strand	105-111	7	9
β-strand	121-122	2	10
β-strand	126-136	11	10
β-strand	143-151	9	10
β-strand	155	1	12
α-helix	156-158	3
α-helix	162-163	2
β-strand	164-170	7	13
β-strand	174-180	7	13
β-strand	184-186	3	14
β-strand	190-200	11	13
β-strand	204-219	16	15
β-strand	222-237	16	15
β-strand	245-251	7	13
α-helix	252-255	4
α-helix	258-260	3
β-strand	261-264	4	15
β-strand	268-280	13	15
β-strand	285-288	4	15
β-strand	291-292	2	15
β-strand	293-295	3	14
β-strand	297	1	12

Chains G and L: 12 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	14-17	4
α-helix	18-22	5
α-helix	24-25	2
β-strand	29-39	11	16
α-helix	42-44	3
β-strand	46-55	10	16
β-strand	64-70	7	16
α-helix	71-80	10
α-helix	81-85	5
α-helix	89-92	4
α-helix	97-100	4
α-helix	108-110	3
α-helix	112-131	20
α-helix	133-137	5
α-helix	139-146	8

Chains H and N: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	554-556	3	15
α-helix	557	1
β-strand	558-559	2	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 26A	F, J	protein	294	Homo sapiens	O75436 (AlphaFold model)
Sorting nexin-3	G, L	protein	155	Mus musculus	O60493 (AlphaFold model)
C-term (residues 493-54) of Wls (fitted sequence corresponds to hDMT1-II)	H, N	protein	10	Mus musculus	P49281 (AlphaFold model)
Vacuolar protein sorting-associated protein 35	A, C	protein	352	Homo sapiens	Q96QK1 (AlphaFold model)

Sequence of entity 1 (F, J), FASTA

>7BLO_1 Vacuolar protein sorting-associated protein 26A (chains F, J)
FGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQG
IRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVR
LRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHL
KDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIP
IRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDEEDRRYFKQQEIILWRKAPEK

Sequence of entity 2 (G, L), FASTA

>7BLO_2 Sorting nexin-3 (chains G, L)
TVADTRRLITKPQNLNDAYGPPSNFLEIDVSNPQTVGVGRGRFTTYEIRVKTNLPIFKLK
ESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDNFIEERKQGLE
QFINKVAGHPLAQNERCLHMFLQDEIIDKSYTPSK

Sequence of entity 3 (H, N), FASTA

>7BLO_3 C-term (residues 493-54) of Wls (fitted sequence corresponds to hDMT1-II) (chains H, N)
QPELYLLNTM

Sequence of entity 4 (A, C), FASTA

>7BLO_4 Vacuolar protein sorting-associated protein 35 (chains A, C)
QEKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELRTSMLSPKSYYELYMAIS
DELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVKSFPQSRKDILK
DLVEMCRGVQHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFAEMN
KLWVRMQHQGHSRDREKRERERQELRILVGTNLVRLSQLEGVNVERYKQIVLTGILEQVV
NCRDALAQEYLMECIIQVFPDEFHLQTLNPFLRACAELHQNVNVKNIIIALIDRLALFAH
REDGPGIPADIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLINLAMKCYP

Ligands and cofactors

ID	Name	Formula	Copies
PIB	2-(butanoyloxy)-1-{[(HYDROXY{[2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]o…	C17 H32 O16 P2	2

Primary citation

Architecture and mechanism of metazoan retromer:SNX3 tubular coat assembly. Leneva, N., Kovtun, O., Morado, D.R. et al. Sci Adv (2021) 7. DOI 10.1126/sciadv.abf8598 · PubMed

Other PDB entries of the same protein (UniProt O75436 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2FAU 2.1 Å, Crystal structure of human vps26
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)
5F0M 3.1 Å, Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled)
9Q8M 3.13 Å, VPS35-VPS26-SNX12 Complex
5F0L 3.2 Å, Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1

Browse structure collections

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