7LIA | pdb_00007lia

5-HT bound serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in outward facing conformation

PDB DOI: https://doi.org/10.2210/pdb7LIA/pdb
EM Map EMD-23365: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Mus musculus
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2021-01-26 Released: 2021-12-15
Deposition Author(s): Yang, D., Gouaux, E.
Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Illumination of serotonin transporter mechanism and role of the allosteric site.

Yang, D., Gouaux, E.

(2021) Sci Adv 7: eabl3857-eabl3857

PubMed: 34851672 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abl3857
Primary Citation Related Structures:
7LI6, 7LI7, 7LI8, 7LI9, 7LIA, 7MGW

PubMed Abstract:
The serotonin transporter (SERT) terminates serotonin signaling by using sodium and chloride gradients to drive reuptake of serotonin into presynaptic neurons and is the target of widely used medications to treat neuropsychiatric disorders. Despite decades of study, the molecular mechanism of serotonin transport, the coupling to ion gradients, and the role of the allosteric site have remained elusive. Here, we present cryo–electron microscopy structures of SERT in serotonin-bound and serotonin-free states, in the presence of sodium or potassium, resolving all fundamental states of the transport cycle. From the SERT-serotonin complex, we localize the substrate-bound allosteric site, formed by an aromatic pocket positioned in the scaffold domain in the extracellular vestibule, connected to the central site via a short tunnel. Together with elucidation of multiple apo state conformations, we provide previously unseen structural understanding of allosteric modulation, demonstrating how SERT binds serotonin from synaptic volumes and promotes unbinding into the presynaptic neurons.

Organizational Affiliation

Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA.

Macromolecule Content

Total Structure Weight: 88.96 kDa
Atom Count: 6,279
Modeled Residue Count: 767
Deposited Residue Count: 767
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-dependent serotonin transporter	A	539	Homo sapiens	Mutation(s): 0 Gene Names: SLC6A4, HTT, SERT Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P31645 (Homo sapiens) Explore P31645 Go to UniProtKB: P31645
PHAROS: P31645 GTEx: ENSG00000108576
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31645
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: P31645-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
variable domain of 15B8 antibody Fab heavy chain	B	118	Mus musculus	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
variable domain of 15B8 antibody Fab light chain	C	110	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain CA [auth A] MOL2 format, chain CA [auth A] mmCIF format, chain CA [auth A]	CA [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain CA [auth A] Interactions & Density Focus chain CA [auth A]
SRO (Subject of Investigation/LOI) Query on SRO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A]	E [auth A], I [auth A]	SEROTONIN C₁₀ H₁₂ N₂ O QZAYGJVTTNCVMB-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain I [auth A]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain J [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain J [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain J [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A]	AA [auth A], BA [auth A], J [auth A], V [auth A], W [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain J [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain J [auth A] Focus chain V [auth A] Focus chain W [auth A]
HP6 Query on HP6 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain X [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A]	K [auth A] L [auth A] M [auth A] N [auth A] O [auth A] K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], X [auth A], Y [auth A], Z [auth A]	HEPTANE C₇ H₁₆ IMNFDUFMRHMDMM-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
LNK Query on LNK Download:Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A] mmCIF format, chain U [auth A]	U [auth A]	PENTANE C₅ H₁₂ OFBQJSOFQDEBGM-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]