7LI6: Apo SERT reconstituted in lipid nanodisc in KCl

apo SERT reconstituted in lipid nanodisc in KCl. Determined by electron microscopy at 3.5 Å resolution. Released 15 Dec 2021.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 6,249
Mol. weight: 88.87 kDa
Ligands: D12, D10, HP6, R16
Released: 15 Dec 2021

Explore 7LI6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LI6 contains 36 α-helices and 33 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: 35 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	83-86	4
α-helix	89-92	4
α-helix	104-111	8
α-helix	118-128	11
α-helix	130-142	13
α-helix	150-152	3
α-helix	160-189	30
β-strand	209	1	1
β-strand	225	1	1
α-helix	227-231	5
α-helix	232-236	5
β-strand	244	1	2
β-strand	247	1	2
β-strand	251	1	3
α-helix	253-267	15
α-helix	281-284	4
α-helix	286-300	15
α-helix	306-312	7
α-helix	318-321	4
α-helix	326-337	12
α-helix	343-347	5
α-helix	361-390	30
α-helix	394-396	3
α-helix	405-414	10
α-helix	420-442	23
α-helix	444-453	10
α-helix	458-461	4
α-helix	464-475	12
β-strand	482	1	3
α-helix	485-489	5
α-helix	491-494	4
α-helix	499-510	12
α-helix	511-515	5
α-helix	518-529	12
α-helix	535-539	5
α-helix	540-544	5
α-helix	545-558	14
β-strand	565	1	4
β-strand	568	1	4
α-helix	573-584	12
α-helix	588-599	12
α-helix	604-612	9
α-helix	614-616	3

Chain B: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	5
β-strand	29	1	6
β-strand	37-44	8	5
α-helix	48-50	3
β-strand	53-58	6	7
β-strand	64-70	7	7
β-strand	77-79	3	7
β-strand	89-90	2	5
β-strand	97-102	6	5
β-strand	112-113	2	7
β-strand	116-117	2	7
β-strand	130	1	7
β-strand	134-135	2	7
β-strand	136	1	6

Chain C: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	8
β-strand	30-31	2	9
β-strand	43-44	2	8
β-strand	57-61	5	10
β-strand	62	1	9
β-strand	69-73	5	10
β-strand	77-78	2	10
β-strand	87-89	3	11
β-strand	96-98	3	11
β-strand	109-110	2	9
β-strand	112-114	3	10
β-strand	126-128	3	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium-dependent serotonin transporter	A	protein	539	Homo sapiens	P31645 (AlphaFold model)
variable domain of 15B8 antibody Fab heavy chain	B	protein	118	Mus musculus
variable domain of 15B8 antibody Fab light chain	C	protein	110	Mus musculus

Sequence of entity 1 (A), FASTA

>7LI6_1 Sodium-dependent serotonin transporter (chains A)
RETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLPYTIMAIFGGIPLFYMELA
LGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTDQLPWT
SCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISWQLALC
IMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIILSVLLVRGATLPGAWRGVLFYLKPNWQ
KLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSFVSGFV
IFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAIIFFLMLITLGLDS
TFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLEEYATG
PAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFIICSFLM
SPPQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIITPGTFKERIIKSITPETP

Sequence of entity 2 (B), FASTA

>7LI6_2 variable domain of 15B8 antibody Fab heavy chain (chains B)
QVQLQQSGPELVKLGASVRISCKASGYRFSYSWMNWVKQRPGKGLEWIGRIYPGDGDTKY
SGKFKGKATLTADKSSSTVYMQLSSLTSEDSAVYFCARSAYGSEGFAMDYWGQGTSVT

Sequence of entity 3 (C), FASTA

>7LI6_3 variable domain of 15B8 antibody Fab light chain (chains C)
DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFLNWFQQKPGQPPKLLIYAASNQGS
GVPARFSGSGSGTYFSLNIHPMEEDDTAVYFCQQTKGVSWTFGGGTKVEI

Ligands and cofactors

ID	Name	Formula	Copies
D12	Dodecane	C12 H26	3
D10	Decane	C10 H22	6
HP6	Heptane	C7 H16	9
R16	Hexadecane	C16 H34	1
LNK	Pentane	C5 H12	4

Water and common crystallization additives (CL) are not listed.

Primary citation

Illumination of serotonin transporter mechanism and role of the allosteric site. Yang, D., Gouaux, E. Sci Adv (2021) 7:eabl3857-eabl3857. DOI 10.1126/sciadv.abl3857 · PubMed

Other PDB entries of the same protein (UniProt P31645 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9HCO 2.78 Å, Outward-open structure of human serotonin transporter bound to vilazodone
7TXT 3.0 Å, Structure of human serotonin transporter bound to small molecule '8090 in lipid nanodisc…
5I6X 3.14 Å, X-ray structure of the ts3 human serotonin transporter complexed with paroxetine at the…
5I71 3.15 Å, X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram at…
9VWS 3.2 Å, Cryo-EM structure of human serotonin transporter in complex with tesofensine
5I73 3.24 Å, X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram at…
9IY7 3.27 Å, Cryo-EM structure of the wild-type human serotonin transporter complexed with S-ketamine
6VRH 3.3 Å, Cryo-EM structure of the wild-type human serotonin transporter complexed with paroxetine…
7LIA 3.3 Å, 5-HT bound serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in…
5I74 3.4 Å, X-ray structure of the ts3 human serotonin transporter complexed with Br-citalopram at…
9PNS 3.4 Å, Structure of human serotonin transporter bound to small molecule zPZd in lipid nanodisc…
5I75 3.49 Å, X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram at…

Browse structure collections

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