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- PDB-6awn: X-ray structure of the S439T human serotonin transporter complexe... -

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Basic information

Entry
Database: PDB / ID: 6awn
TitleX-ray structure of the S439T human serotonin transporter complexed with paroxetine at the central site
Components
  • (8B6 antibody FAB ...) x 2
  • Sodium-dependent serotonin transporter
KeywordsTRANSPORT PROTEIN / Neurotransmitter transporter / antidepressant
Function / homology
Function and homology information


negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / Serotonin clearance from the synaptic cleft / serotonergic synapse / positive regulation of serotonin secretion / cocaine binding / sperm ejaculation / serotonin:sodium:chloride symporter activity / negative regulation of synaptic transmission, dopaminergic / neurotransmitter transmembrane transporter activity ...negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / Serotonin clearance from the synaptic cleft / serotonergic synapse / positive regulation of serotonin secretion / cocaine binding / sperm ejaculation / serotonin:sodium:chloride symporter activity / negative regulation of synaptic transmission, dopaminergic / neurotransmitter transmembrane transporter activity / enteric nervous system development / serotonin uptake / cellular response to cGMP / negative regulation of organ growth / sodium ion binding / monoamine transmembrane transporter activity / monoamine transport / serotonin binding / vasoconstriction / brain morphogenesis / neurotransmitter transport / antiporter activity / syntaxin-1 binding / nitric-oxide synthase binding / membrane depolarization / social behavior / negative regulation of neuron differentiation / sodium ion transmembrane transport / endomembrane system / monoatomic cation channel activity / positive regulation of cell cycle / cellular response to retinoic acid / response to nutrient / response to toxic substance / memory / platelet aggregation / circadian rhythm / actin filament binding / integrin binding / response to estradiol / presynaptic membrane / postsynaptic membrane / endosome membrane / response to hypoxia / neuron projection / response to xenobiotic stimulus / immune response / membrane raft / focal adhesion / synapse / positive regulation of gene expression / extracellular space / 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. / Immunoglobulin V-Type / Immunoglobulin V-set domain ...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. / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Paroxetine / CHOLESTEROL / MAb 106 heavy chain / MAb 110 light chain / Sodium-dependent serotonin transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 Å
AuthorsColeman, J.A. / Gouaux, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)5R37MH070039 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structural basis for recognition of diverse antidepressants by the human serotonin transporter.
Authors: Coleman, J.A. / Gouaux, E.
History
DepositionSep 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.2Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 31, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.4Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.6Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Jul 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _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 1.8Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 FAB heavy chain
C: 8B6 antibody FAB light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,00310
Polymers110,2763
Non-polymers1,7277
Water0
1
A: Sodium-dependent serotonin transporter
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)112,00310
Polymers110,2763
Non-polymers1,7277
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+5/21
Buried area7210 Å2
ΔGint-51 kcal/mol
Surface area41060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.150, 162.840, 140.820
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: 61703.789 Da / Num. of mol.: 1 / Fragment: residues 76-618 / Mutation: Y110A, I291A, C554A, C580A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A4, HTT, SERT / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P31645

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Antibody , 2 types, 2 molecules BC

#2: Antibody 8B6 antibody FAB heavy chain


Mass: 24853.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: HC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0F7R1P3
#3: Antibody 8B6 antibody FAB 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) / Gene: LC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0F7R5U8

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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 / N-Acetylglucosamine


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: isolated from a genetically manipulated source
Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 4 types, 4 molecules

#5: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


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


Mass: 329.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C19H20FNO3 / Comment: antidepressant, inhibitor*YM
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Na

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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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl pH 8.5, 40 mM Li2S04, 40 mM Na2S04, 34.5% 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: Aug 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.62→53.258 Å / Num. obs: 28860 / % possible obs: 92.6 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.98
Reflection shellResolution: 3.62→3.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.73 / Num. unique obs: 1529 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2597)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5i6x

5i6x


Resolution: 3.62→53.258 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 31.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 1448 5.02 %
Rwork0.2559 --
obs0.2562 28860 88.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.62→53.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7599 0 104 0 7703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097936
X-RAY DIFFRACTIONf_angle_d1.05710844
X-RAY DIFFRACTIONf_dihedral_angle_d17.1752740
X-RAY DIFFRACTIONf_chiral_restr0.2181232
X-RAY DIFFRACTIONf_plane_restr0.0071327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.62-3.74940.37411270.38242352X-RAY DIFFRACTION76
3.7494-3.89950.36841300.35432489X-RAY DIFFRACTION80
3.8995-4.07690.38611280.34012601X-RAY DIFFRACTION84
4.0769-4.29170.33661450.29152722X-RAY DIFFRACTION88
4.2917-4.56050.26271500.2742824X-RAY DIFFRACTION91
4.5605-4.91240.30881470.25532865X-RAY DIFFRACTION93
4.9124-5.40630.30421540.25882890X-RAY DIFFRACTION93
5.4063-6.18760.30191520.26912888X-RAY DIFFRACTION93
6.1876-7.79180.27821580.26452890X-RAY DIFFRACTION93
7.7918-53.26360.18871570.20712891X-RAY DIFFRACTION93

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