6dzz

Cryo-EM Structure of the wild-type human serotonin transporter in complex with ibogaine and 15B8 Fab in the inward conformation

Method: ELECTRON MICROSCOPY D_max: 113.0 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sodium-dependent serotonin transporter

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 78–617	Fragment：UNP residues 79-615	15B8 antibody heavy chain × 1 15B8 antibody light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 HJM (5beta)-12-methoxyibogamine × 1 LMT DODECYL-BETA-D-MALTOSIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6DZZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5I6X X-ray structure of the ts3 human serotonin transporter complexed with paroxetine at the central site Deposited 2016-02-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 76–618（543 aa）	Mutation：Y110A, I291A, T439S	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CLR CHOLESTEROL × 1 LMT DODECYL-BETA-D-MALTOSIDE × 1 8PR Paroxetine × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM Tris pH 8.5, 25-125 mM KCl, 32.5-34% PEG 400, 0.5% 6-aminohexanoic acid	Resolution 3.14 Å R-free 0.270
5I6Z X-ray structure of the ts2 human serotonin transporter Deposited 2016-02-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 76–618（543 aa）	Mutation：I291A, T439S	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM Tris pH 8, 250 mM LiCl, 34.7% PEG 400	Resolution 4.53 Å R-free 0.317
5I71 X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram at the central site Deposited 2016-02-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 76–618（543 aa）	Not recorded	68P (1S)-1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CLR CHOLESTEROL × 1 D12 DODECANE × 1 HEX HEXANE × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM Tris pH 8.5, 25-125 mM KCl, 32.5-34% PEG 400, 0.5% 6-aminohexanoic acid	Resolution 3.15 Å R-free 0.276
5I73 X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram at the central and allosteric sites Deposited 2016-02-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 76–618（543 aa）	Not recorded	68P (1S)-1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CLR CHOLESTEROL × 1 C14 TETRADECANE × 1 NA SODIUM ION × 2 ACA 6-AMINOHEXANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM Tris pH 8.5, 25-125 mM KCl, 32.5-34% PEG 400	Resolution 3.24 Å R-free 0.275
5I74 X-ray structure of the ts3 human serotonin transporter complexed with Br-citalopram at the central site Deposited 2016-02-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 76–618（543 aa）	Not recorded	69D (1S)-1-(4-bromophenyl)-1-[3-(dimethylamino)propyl]-1,3-dihydro-2-benzofuran-5-carbonitrile × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CLR CHOLESTEROL × 1 D12 DODECANE × 1 HEX HEXANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM Tris pH 8.5, 125 mM NaCl, 125 mM magnesium chloride, 33.4% PEG 400	Resolution 3.40 Å R-free 0.296
5I75 X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram at the central site and Br-citalopram at the allosteric site Deposited 2016-02-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 76–618（543 aa）	Not recorded	68P (1S)-1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CLR CHOLESTEROL × 1 C14 TETRADECANE × 1 69D (1S)-1-(4-bromophenyl)-1-[3-(dimethylamino)propyl]-1,3-dihydro-2-benzofuran-5-carbonitrile × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM Tris pH 8.5, 25-125 mM KCl, 32.5-34% PEG 400, 0.5% 6-aminohexanoic acid	Resolution 3.49 Å R-free 0.286
6AWN X-ray structure of the S439T human serotonin transporter complexed with paroxetine at the central site Deposited 2017-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 76–618（543 aa） Fragment：residues 76-618	Mutation：Y110A, I291A, C554A, C580A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CLR CHOLESTEROL × 1 LMT DODECYL-BETA-D-MALTOSIDE × 1 8PR Paroxetine × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Tris-HCl pH 8.5, 40 mM Li2S04, 40 mM Na2S04, 34.5% PEG 400, 0.5% 6-aminohexanoic acid	Resolution 3.62 Å R-free 0.263
6AWO X-ray structure of the ts3 human serotonin transporter complexed with sertraline at the central site Deposited 2017-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 76–618（543 aa）	Mutation：Y110A, I291A, T439S, C554A, C580A	SRE (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CLR CHOLESTEROL × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；50 mM Tris-HCl pH 8.5, 75 mM Li2SO4, 75 mM Na2SO4, 35% PEG 400, 0.5% 6-aminohexanoic acid	Resolution 3.53 Å R-free 0.283
6AWP X-ray structure of the ts3 human serotonin transporter complexed with fluvoxamine at the central site Deposited 2017-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 76–618（543 aa） Fragment：residues 76-618	Mutation：Y110A, I291A, T439S, C554A, C580A	FVX Fluvoxamine × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CLR CHOLESTEROL × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；50 mM Tris-HCl pH 8.5, 75 mM Li2SO4, 75 mM Na2SO4, 34% PEG 400, 0.5% 6-aminohexanoic acid	Resolution 3.80 Å R-free 0.269
6AWQ Anomalous chloride signal reveals the position of sertraline complexed with the serotonin transporter at the central site Deposited 2017-09-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 76–618（543 aa）	Not recorded	SRE (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CLR CHOLESTEROL × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；50 mM Tris-HCl pH 8.5, 40 mM Li2SO4, 40 mM Na2SO4, 35% PEG 400, 0.5% 6-aminohexanoic acid	Resolution 4.05 Å R-free 0.316
6DZV Wild type human serotonin transporter in complex with 15B8 Fab bound to ibogaine in occluded conformation Deposited 2018-07-05	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 79–615（537 aa） Fragment：UNP residues 79-615	Not recorded	HJM (5beta)-12-methoxyibogamine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6DZW Cryo-EM structure of the ts2-inactive human serotonin transporter in complex with paroxetine and 15B8 Fab and 8B6 ScFv Deposited 2018-07-05	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 79–615（537 aa）	Not recorded	8PR Paroxetine × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
6DZY Cryo-EM structure of the ts2-active human serotonin transporter in complex with 15B8 Fab and 8B6 ScFv bound to ibogaine Deposited 2018-07-05	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 79–615（537 aa） Fragment：UNP residues 79-615	Not recorded	HJM (5beta)-12-methoxyibogamine × 1 LMT DODECYL-BETA-D-MALTOSIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6VRH Cryo-EM structure of the wild-type human serotonin transporter complexed with paroxetine and 8B6 Fab Deposited 2020-02-07	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–630（630 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 8PR Paroxetine × 1 CL CHLORIDE ION × 1 LMT DODECYL-BETA-D-MALTOSIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
6VRK Cryo-EM structure of the wild-type human serotonin transporter complexed with Br-paroxetine and 8B6 Fab Deposited 2020-02-07	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–630（630 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 LMT DODECYL-BETA-D-MALTOSIDE × 1 RFS Br-paroxetine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6VRL Cryo-EM structure of the wild-type human serotonin transporter complexed with I-paroxetine and 8B6 Fab Deposited 2020-02-07	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–630（630 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 LMT DODECYL-BETA-D-MALTOSIDE × 1 RFY I-paroxetine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6W2B Anomalous bromine signal reveals the position of Br-paroxetine complexed with the serotonin transporter at the central site Deposited 2020-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 76–618（543 aa） Fragment：UNP residues 76-618	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 RFS Br-paroxetine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；50 mM Tris, pH 8.5, 20 mM sodium sulfate, 20 mM lithium chloride, 36% PEG400, 0.5% 6-aminohexanoic acid	Resolution 4.70 Å R-free 0.293
6W2C Anomalous iodine signal reveals the position of I-paroxetine complexed with the serotonin transporter at the central site Deposited 2020-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 76–618（543 aa） Fragment：UNP residues 76-618	Not recorded	RFY I-paroxetine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM HEPES, pH 7.5, 40 mM magnesium chloride, 32% PEG400	Resolution 6.30 Å R-free 0.369
7LI6 apo SERT reconstituted in lipid nanodisc in KCl Deposited 2021-01-26	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 79–617（539 aa）	Not recorded	CL CHLORIDE ION × 1 R16 HEXADECANE × 1 HP6 HEPTANE × 9 D10 DECANE × 6 D12 DODECANE × 3 LNK PENTANE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7LI7 apo serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in occluded conformation Deposited 2021-01-26	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 79–615（537 aa）	Not recorded	D12 DODECANE × 3 HP6 HEPTANE × 5 LNK PENTANE × 1 CLR CHOLESTEROL × 1 D10 DECANE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
7LI8 apo serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in inward open conformation Deposited 2021-01-26	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 79–617（539 aa）	Not recorded	R16 HEXADECANE × 1 D10 DECANE × 1 D12 DODECANE × 3 HP6 HEPTANE × 6 LNK PENTANE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7LI9 5-HT bound serotonin transporter reconstituted in lipid nanodisc in KCl Deposited 2021-01-26	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 79–617（539 aa）	Not recorded	D12 DODECANE × 2 HP6 HEPTANE × 2 D10 DECANE × 3 LNK PENTANE × 1 SRO SEROTONIN × 2 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7LIA 5-HT bound serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in outward facing conformation Deposited 2021-01-26	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 79–617（539 aa）	Not recorded	SRO SEROTONIN × 2 CL CHLORIDE ION × 1 NA SODIUM ION × 2 D10 DECANE × 5 HP6 HEPTANE × 13 LNK PENTANE × 1 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7LWD Cryo-EM structure of the wild-type human serotonin transporter complexed with vilazodone, imipramine and 15B8 Fab Deposited 2021-03-01	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 77–617（541 aa）	Not recorded	IXX 3-(5H-DIBENZO[B,F]AZEPIN-5-YL)-N,N-DIMETHYLPROPAN-1-AMINE × 1 YG7 5-{4-[4-(5-cyano-1H-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å
7MGW 5-HT bound serotonin transporter reconstituted in lipid nanodisc in NaCl in occluded conformation Deposited 2021-04-13	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 79–615（537 aa）	Not recorded	CL CHLORIDE ION × 1 D12 DODECANE × 4 LNK PENTANE × 1 HP6 HEPTANE × 6 D10 DECANE × 1 SRO SEROTONIN × 2 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7TXT Structure of human serotonin transporter bound to small molecule '8090 in lipid nanodisc and NaCl Deposited 2022-02-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 77–617（541 aa）	Not recorded	KWC 1-[4-(4-fluorophenyl)-1,3-thiazol-2-yl]piperazine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9HCO Outward-open structure of human serotonin transporter bound to vilazodone Deposited 2024-11-11	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–630（630 aa）	Not recorded	YG7 5-{4-[4-(5-cyano-1H-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide × 1 NA SODIUM ION × 2 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.78 Å
9IY7 Cryo-EM structure of the wild-type human serotonin transporter complexed with S-ketamine Deposited 2024-07-30	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–630（630 aa）	Not recorded	CL CHLORIDE ION × 1 NA SODIUM ION × 2 Y01 CHOLESTEROL HEMISUCCINATE × 3 LMT DODECYL-BETA-D-MALTOSIDE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 JC9 (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one × 1 DD9 nonane × 5 D12 DODECANE × 6 D10 DECANE × 2 OCT N-OCTANE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å
9PNS Structure of human serotonin transporter bound to small molecule zPZd in lipid nanodisc and NaCl Deposited 2025-07-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 77–617（541 aa）	Not recorded	CL CHLORIDE ION × 1 A1CIZ (6M)-1-methyl-6-(1,2,5,6-tetrahydropyridin-3-yl)-1H-indole × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

29 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SC6A4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–540； UniProt 78–617

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6dzz
Deposition date deposition_date	2018-07-05
Structure title title	Cryo-EM Structure of the wild-type human serotonin transporter in complex with ibogaine and 15B8 Fab in the inward conformation
Keywords keywords	ibogaine, human serotonin transporter, Fab, TRANSPORT PROTEIN-IMMUNE SYSTEM complex; TRANSPORT PROTEIN/IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.79 Å
Radius of gyration Rg (electron density) rg_electron	32.38 Å
Forward intensity I(0) i0	102927000.00
Molecular weight molecular_weight	86886.0 kDa
Excluded volume excluded_volume	111130 Å³
Envelope volume envelope_volume	143890 Å³
Hydration-shell volume shell_volume	38642 Å³
Envelope diameter envelope_diameter	122.4 Å
Shell Rg shell_rg	37.68 Å
Envelope Rg envelope_rg	32.77 Å
Shape Rg shape_rg	32.33 Å
Total Rg total_rg	33.00 Å
Total atoms total_atoms	6141
Residues n_residues	768
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	113.0 Å
Rg (real space) rg_real	33.07 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	1.0290e+08
I(0) uncertainty (real space) i0_real_error	1.6460e+06
Rg (reciprocal space) rg_reciprocal	32.96 Å
I(0) (reciprocal space) i0_reciprocal	102900000.0000
Solution quality estimate total_estimate	0.8389
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.0 Å
Skewness Skewness skewness	0.527
Kurtosis Kurtosis kurtosis	-0.314
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31560000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.736; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.830; Smooth: 0.863

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Sodium-dependent serotonin transporter
Molecular weight formula_weight	61005.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6141

ERETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLPYTIMAIFGGIPLFYMELALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTDQLPWTSCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISWQLALCIMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIILSVLLVRGATLPGAWRGVLFYLKPNWQKLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSFVSGFVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAIIFFLMLITLGLDSTFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLEEYATGPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFIICSFLMSPPQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIITPGTFKERIIKSITPETP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	15B8 antibody heavy chain
Molecular weight formula_weight	12980.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QVQLQQSGPELVKLGASVRISCKASGYRFSYSWMNWVKQRPGKGLEWIGRIYPGDGDTKYSGKFKGKATLTADKSSSTVYMQLSSLTSEDSAVYFCARSAYGSEGFAMDYWGQGTSVT

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Mus musculus

Entity 3 Entity 3 polymer

Description description	15B8 antibody light chain
Molecular weight formula_weight	11776.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFLNWFQQKPGQPPKLLIYAASNQGSGVPARFSGSGSGTYFSLNIHPMEEDDTAVYFCQQTKGVSWTFGGGTKVEI

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Mus musculus

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	(5beta)-12-methoxyibogamine
Molecular weight formula_weight	310.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.60 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	368656

fit	/app/data/saxs_computation/dz/6dzz/6dzz.fit
pddf	/app/data/pr_computation/dz/6dzz/6dzz.pr.out
profile	/app/data/saxs_computation/dz/6dzz/6dzz.dat

Cryo-EM Structure of the wild-type human serotonin transporter in complex with ibogaine and 15B8 Fab in the inward conformation

1. Protein Identity and Related Structures Protein Identity & Related Structures

Sodium-dependent serotonin transporter

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)