9IY7 | pdb_00009iy7

Cryo-EM structure of the wild-type human serotonin transporter complexed with S-ketamine

PDB DOI: https://doi.org/10.2210/pdb9IY7/pdb
EM Map EMD-60987: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-07-30 Released: 2025-11-12
Deposition Author(s): Ning, Y., Ge, J.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9IY7

This is version 1.1 of the entry. See complete history.

Literature

CryoEM structure of a transmembrane protein

Ning, Y., Ge, J.

To be published.

Macromolecule Content

Total Structure Weight: 76.13 kDa
Atom Count: 4,664
Modeled Residue Count: 540
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-dependent serotonin transporter	A	636	Homo sapiens	Mutation(s): 0 Gene Names: SLC6A4, HTT, SERT
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

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain W [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain W [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain W [auth A]	E [auth A], F [auth A], W [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain W [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain W [auth A]
JC9 (Subject of Investigation/LOI) Query on JC9 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	(2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one C₁₃ H₁₆ Cl N O YQEZLKZALYSWHR-ZDUSSCGKSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
D12 Query on D12 Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain Y [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain T [auth A] mmCIF format, chain V [auth A] mmCIF format, chain Y [auth A]	AA [auth A] L [auth A] N [auth A] T [auth A] V [auth A] AA [auth A], L [auth A], N [auth A], T [auth A], V [auth A], Y [auth A]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain T [auth A] Focus chain V [auth A] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain T [auth A] Focus chain V [auth A] Focus chain Y [auth A]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain U [auth A] MOL2 format, chain O [auth A] MOL2 format, chain U [auth A] mmCIF format, chain O [auth A] mmCIF format, chain U [auth A]	O [auth A], U [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain U [auth A] Interactions & Density Focus chain O [auth A] Focus chain U [auth A]
DD9 Query on DD9 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain X [auth A] SDF format, chain Z [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Z [auth A]	J [auth A], K [auth A], M [auth A], X [auth A], Z [auth A]	nonane C₉ H₂₀ BKIMMITUMNQMOS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain X [auth A] Focus chain Z [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain X [auth A] Focus chain Z [auth A]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain BA [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] MOL2 format, chain BA [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] mmCIF format, chain BA [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]	BA [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain BA [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		LG-QS-202203-05; 22PJ1410300

Revision History (Full details and data files)

Version 1.0: 2025-11-12
Type: Initial release
Version 1.1: 2025-12-10
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.