7BLQ: Vacuolar protein sorting-associated protein 35

Vps26 dimer region of the fungal membrane-assembled retromer:Grd19 complex. Determined by electron microscopy at 9.2 Å resolution. Released 3 Mar 2021.

Method: Electron microscopy
Resolution: 9.2 Å
Organisms: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719), Chaetomium thermophilum var. thermophilum DSM 1495
Chains: 8
Atoms: 11,722
Mol. weight: 167.25 kDa
Ligands: PIB
Released: 3 Mar 2021

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

Secondary structure: helices and β-sheets

7BLQ contains 61 α-helices and 60 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	13-33	21
α-helix	38-49	12
α-helix	50-53	4
α-helix	59-86	28
α-helix	92-95	4
α-helix	96-98	3
α-helix	102-119	18
α-helix	124-134	11
α-helix	135-137	3
α-helix	141-155	15
α-helix	171-194	24
α-helix	198-200	3
α-helix	201-222	22
α-helix	228-231	4
α-helix	232-236	5
α-helix	237-246	10
α-helix	250-262	13
α-helix	265-269	5
α-helix	272-279	8
α-helix	288-304	17

Chain C: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	13-33	21
α-helix	38-49	12
α-helix	50-53	4
α-helix	59-86	28
α-helix	92-95	4
α-helix	96-98	3
α-helix	102-119	18
α-helix	124-134	11
α-helix	141-154	14
α-helix	171-194	24
α-helix	198-200	3
α-helix	201-223	23
α-helix	228-231	4
α-helix	232-236	5
α-helix	237-246	10
α-helix	250-262	13
α-helix	265-269	5
α-helix	272-279	8
α-helix	288-304	17

Chains F and J: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	10
β-strand	23-28	6	11
α-helix	29-31	3
β-strand	32-37	6	11
β-strand	38-40	3	12
β-strand	45-53	9	10
β-strand	59-61	3	13
β-strand	64-74	11	14
α-helix	78-80	3
β-strand	81-92	12	14
β-strand	95-97	3	13
β-strand	101-107	7	10
β-strand	117-118	2	14
β-strand	122-132	11	14
β-strand	139-145	7	14
β-strand	146-148	3	12
β-strand	160-166	7	15
β-strand	170-176	7	15
β-strand	180-182	3	16
β-strand	186-196	11	15
β-strand	200-215	16	17
β-strand	218-233	16	17
β-strand	241-247	7	15
α-helix	248-250	3
α-helix	253-256	4
β-strand	257-260	4	17
β-strand	264-276	13	17
β-strand	281-288	8	17
β-strand	289-291	3	16
α-helix	293-295	3

Chains G and L: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	76-86	11	1
β-strand	93-102	10	1
β-strand	111-117	7	1
α-helix	118-132	15
α-helix	138-140	3
α-helix	151-170	20
α-helix	172-177	6
α-helix	179-185	7

Chains U and V: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	554-556	3	17
α-helix	557	1
β-strand	558-559	2	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 35	A, C	protein	295	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0S709 (AlphaFold model)
Sorting nexin-3	G, L	protein	116	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0S0X3 (AlphaFold model)
Vacuolar protein sorting-associated protein 26-like protein	F, J	protein	292	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0S0E6 (AlphaFold model)
The C-terminal portion of Kex2 cargo, fitted with Phi-X-(L/M) sorting motif of hDMT1-II cargo.	U, V	protein	10	Chaetomium thermophilum var. thermophilum DSM 1495	P49281 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7BLQ_1 Vacuolar protein sorting-associated protein 35 (chains A, C)
RLLEDALIAVRQQTAMMRKFLDTPGKLMDALKCCSTLVSELRTSSLSPKQYYELYMAVFD
ALRYLSAHLRENHPVNHLADLYELVQYAGNIIPRLYLMITVGTAYMSIDGAPVKELMKDM
MDMSRGVQHPVRGLFLRYYLSGQARDYLPTGDSDGPEGNLQDSINFILTNFVEMNKLWVR
LQHQGHSRERDLRTQERRELQLLVGSNIVRLSQLVDLPTYRDSILGPLLEQIVQCRDILA
QEYLLEVITQVFPDEYHLHTLDQFLGAVSRLNPHVNVKAIVIGMMNRLSDYAERE

Sequence of entity 2 (G, L), FASTA

>7BLQ_2 Sorting nexin-3 (chains G, L)
PPENFLEIEVRNPQTHGVGRHMYTDYEIVCRTNIPAFKLRQSSVRRRYSDFEYFRDILER
ESARVTIPPLPGKVFTNRFSDEVIENRRAGLEKFLKIVVGHPLLQTGSKVLAAFVQ

Sequence of entity 3 (F, J), FASTA

>7BLQ_3 Vacuolar protein sorting-associated protein 26-like protein (chains F, J)
FSTPVDIDIVLADADKRAMVDVKLDKNRREKVPLYMDGESVKGCVTVRPKDGKRLEHTGI
KVQFIGTIEMFFDRGNHYEFLSLVQELAAPGELQHPQTFDFNFKNVEKQYESYNGINVKL
RYFVRVTVSRRMADVIREKDIWVYSYRIPPELNSSIKMDVGIEDCLHIEFEYSKSKYHLK
DVIVGRIYFLLVRLKIKHMELSIIRRETTGVAPNQYNESETLVRFEIMDGSPSRGETIPI
RLFLGGFDLTPTFRDVNKKFSTRYYLSLVLIDEDARRYFKQSEIILYRQPPE

Sequence of entity 4 (U, V), FASTA

>7BLQ_4 The C-terminal portion of Kex2 cargo, fitted with Phi-X-(L/M) sorting motif of hDMT1-II cargo. (chains U, V)
QPELYLLNTM

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 G0S709 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BLR 9.3 Å, Vps35/Vps29 arch of fungal membrane-assembled retromer:Vps5 (SNX-BAR) complex.
7BLP 9.5 Å, Vps35/Vps29 arch of fungal membrane-assembled retromer:Grd19 complex
6H7W 11.4 Å, Model of retromer-Vps5 complex assembled on membrane.

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