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- PDB-5i6x: X-ray structure of the ts3 human serotonin transporter complexed ... -

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Basic information

Entry
Database: PDB / ID: 5i6x
TitleX-ray structure of the ts3 human serotonin transporter complexed with paroxetine at the central site
Components
  • (8B6 antibody, ...) x 2
  • Sodium-dependent serotonin transporter
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / Serotonin clearance from the synaptic cleft / positive regulation of serotonin secretion / serotonergic synapse / negative regulation of synaptic transmission, dopaminergic / cocaine binding / serotonin:sodium:chloride symporter activity / cellular response to cGMP / enteric nervous system development ...negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / Serotonin clearance from the synaptic cleft / positive regulation of serotonin secretion / serotonergic synapse / negative regulation of synaptic transmission, dopaminergic / cocaine binding / serotonin:sodium:chloride symporter activity / cellular response to cGMP / enteric nervous system development / negative regulation of organ growth / sodium ion binding / neurotransmitter transmembrane transporter activity / serotonin uptake / vasoconstriction / monoamine transmembrane transporter activity / monoamine transport / serotonin binding / brain morphogenesis / syntaxin-1 binding / antiporter activity / negative regulation of neuron differentiation / male mating behavior / neurotransmitter transport / nitric-oxide synthase binding / amino acid transport / conditioned place preference / membrane depolarization / monoatomic cation channel activity / behavioral response to cocaine / positive regulation of cell cycle / cellular response to retinoic acid / response to nutrient / endomembrane system / sodium ion transmembrane transport / circadian rhythm / response to toxic substance / platelet aggregation / memory / integrin binding / actin filament binding / response to estradiol / presynaptic membrane / postsynaptic membrane / response to hypoxia / neuron projection / endosome membrane / membrane raft / response to xenobiotic stimulus / focal adhesion / synapse / positive regulation of gene expression / identical protein binding / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter, serotonin, N-terminal / Serotonin (5-HT) neurotransmitter transporter, N-terminus / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / Immunoglobulins / Immunoglobulin-like ...Sodium:neurotransmitter symporter, serotonin, N-terminal / Serotonin (5-HT) neurotransmitter transporter, N-terminus / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Paroxetine / CHOLESTEROL / Sodium-dependent serotonin transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsColeman, J.A. / Green, E.M. / Gouaux, E.
CitationJournal: Nature / Year: 2016
Title: X-ray structures and mechanism of the human serotonin transporter.
Authors: Coleman, J.A. / Green, E.M. / Gouaux, E.
History
DepositionFeb 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2May 4, 2016Group: Database references
Revision 1.3Mar 4, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD / _pdbx_struct_assembly_prop.value
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium-dependent serotonin transporter
B: 8B6 antibody, heavy chain
C: 8B6 antibody, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,82410
Polymers109,0963
Non-polymers1,7277
Water181
1
A: Sodium-dependent serotonin transporter
hetero molecules

B: 8B6 antibody, heavy chain
C: 8B6 antibody, light chain


Theoretical massNumber of molelcules
Total (without water)110,82410
Polymers109,0963
Non-polymers1,7277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area7020 Å2
ΔGint-51 kcal/mol
Surface area40990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.150, 162.830, 140.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sodium-dependent serotonin transporter / SERT / 5HT transporter / 5HTT / Solute carrier family 6 member 4


Mass: 61689.766 Da / Num. of mol.: 1 / Mutation: Y110A, I291A, T439S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A4, HTT, SERT / Production host: Homo sapiens (human) / References: UniProt: P31645

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Antibody , 2 types, 2 molecules BC

#2: Antibody 8B6 antibody, heavy chain


Mass: 23688.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody 8B6 antibody, light chain


Mass: 23718.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)

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Sugars , 2 types, 3 molecules

#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 5 molecules

#5: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#7: Chemical ChemComp-8PR / Paroxetine / (3S,4R)-3-[(1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine


Mass: 329.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20FNO3
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris pH 8.5, 25-125 mM KCl, 32.5-34% PEG 400, 0.5% 6-aminohexanoic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.14→53.17 Å / Num. obs: 49873 / % possible obs: 99.9 % / Redundancy: 17.7 % / Rmerge(I) obs: 0.1261 / Net I/σ(I): 15.2

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Processing

Software
NameVersionClassification
PHENIX(DEV_2000: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.14→53.17 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 31.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 2507 5.03 %
Rwork0.238 --
obs0.24 49873 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.14→53.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7526 0 104 1 7631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0228214
X-RAY DIFFRACTIONf_angle_d0.79810745
X-RAY DIFFRACTIONf_dihedral_angle_d10.4152694
X-RAY DIFFRACTIONf_chiral_restr0.2171221
X-RAY DIFFRACTIONf_plane_restr0.0061320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1401-3.20050.3891370.38662637X-RAY DIFFRACTION100
3.2005-3.26580.4441390.37972605X-RAY DIFFRACTION100
3.2658-3.33680.3931380.3862656X-RAY DIFFRACTION100
3.3368-3.41440.38191400.38152626X-RAY DIFFRACTION100
3.4144-3.49980.36921410.33012650X-RAY DIFFRACTION100
3.4998-3.59440.34751370.3312633X-RAY DIFFRACTION100
3.5944-3.70010.33451440.29452643X-RAY DIFFRACTION100
3.7001-3.81950.31421400.26632634X-RAY DIFFRACTION100
3.8195-3.9560.2811380.24872613X-RAY DIFFRACTION100
3.956-4.11430.3461380.23072632X-RAY DIFFRACTION100
4.1143-4.30150.22421360.20832650X-RAY DIFFRACTION100
4.3015-4.52820.22931420.19432641X-RAY DIFFRACTION100
4.5282-4.81170.24741360.1822615X-RAY DIFFRACTION100
4.8117-5.18290.20591430.18932656X-RAY DIFFRACTION100
5.1829-5.70390.29751380.21522613X-RAY DIFFRACTION100
5.7039-6.5280.30081420.2482647X-RAY DIFFRACTION100
6.528-8.21980.24351400.22932634X-RAY DIFFRACTION100
8.2198-53.17520.21441380.20672581X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.43133.42321.80067.77195.0116.8655-1.1697-0.57140.83550.27450.38450.9742-0.26710.63130.73870.72210.1591-0.11720.88450.08510.6385-54.7444-3.615653.0462
22.5522-2.41312.37459.7215-2.02062.49990.22781.09370.7061-1.8729-1.1987-1.78820.93831.77860.75511.43010.0126-0.01932.15330.48751.6455-23.93224.617545.5737
34.16051.40781.07192.81050.85195.36560.0251-0.6627-1.37240.45630.1851-1.36780.85262.9546-0.04271.10230.58910.10521.47440.25381.3396-44.7465-23.145653.6849
42.6477-1.03071.44382.66373.2746.9982-0.51750.2857-0.061-0.43740.0541-0.8861-0.78862.99640.44031.056-0.31-0.34622.63860.24961.6538-13.5314-2.35955.2694
52.19010.7314-0.72821.27290.48915.8833-0.46060.084-0.4911-0.2459-0.1307-0.27381.17561.18760.390.91850.52990.40361.02820.02661.1477-36.4148-22.26613.0028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN B AND RESID 21:138)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 139:237)
3X-RAY DIFFRACTION3(CHAIN C AND RESID 22:124)
4X-RAY DIFFRACTION4(CHAIN C AND RESID 125:234)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 74:617)

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