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- PDB-6awp: X-ray structure of the ts3 human serotonin transporter complexed ... -

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Basic information

Entry
Database: PDB / ID: 6awp
TitleX-ray structure of the ts3 human serotonin transporter complexed with fluvoxamine 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 / 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 / male mating behavior / negative regulation of neuron differentiation / neurotransmitter transport / nitric-oxide synthase binding / amino acid transport / conditioned place preference / membrane depolarization / immunoglobulin complex / monoatomic cation channel activity / behavioral response to cocaine / cellular response to retinoic acid / positive regulation of cell cycle / endomembrane system / response to nutrient / sodium ion transmembrane transport / circadian rhythm / platelet aggregation / response to toxic substance / memory / integrin binding / actin filament binding / response to estradiol / presynaptic membrane / adaptive immune response / postsynaptic membrane / response to hypoxia / neuron projection / endosome membrane / membrane raft / response to xenobiotic stimulus / focal adhesion / synapse / positive regulation of gene expression / extracellular region / metal ion binding / 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. / : / : ...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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CHOLESTEROL / Fluvoxamine / 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: 3.8 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 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 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 1.3Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jul 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 1.7Oct 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
Revision 1.8Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)111,49010
Polymers110,2623
Non-polymers1,2297
Water181
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)111,49010
Polymers110,2623
Non-polymers1,2297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+5/21
Buried area6600 Å2
ΔGint-59 kcal/mol
Surface area41320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.490, 163.860, 140.950
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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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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Protein / Sugars , 2 types, 3 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 / Fragment: residues 76-618 / Mutation: Y110A, I291A, T439S, 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
#5: 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

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Non-polymers , 5 types, 6 molecules

#4: Chemical ChemComp-FVX / Fluvoxamine / 2-[({(1E)-5-methoxy-1-[4-(trifluoromethyl)phenyl]pentylidene}amino)oxy]ethanamine


Mass: 318.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21F3N2O2
#6: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#7: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: 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: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 50 mM Tris-HCl pH 8.5, 75 mM Li2SO4, 75 mM Na2SO4, 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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.8→30 Å / Num. obs: 24814 / % possible obs: 95.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.36
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 1328 / % possible all: 95.7

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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: 3.8→29.443 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 35.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2693 1253 5.05 %
Rwork0.2453 --
obs0.2466 24814 87.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→29.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7598 0 81 1 7680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087907
X-RAY DIFFRACTIONf_angle_d0.98210800
X-RAY DIFFRACTIONf_dihedral_angle_d16.8432742
X-RAY DIFFRACTIONf_chiral_restr0.2191220
X-RAY DIFFRACTIONf_plane_restr0.0071327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8001-3.95190.43581140.40682206X-RAY DIFFRACTION74
3.9519-4.13130.40651350.36312396X-RAY DIFFRACTION80
4.1313-4.34840.35451310.3042536X-RAY DIFFRACTION83
4.3484-4.61990.29111420.25922627X-RAY DIFFRACTION88
4.6199-4.9750.29151400.24492684X-RAY DIFFRACTION90
4.975-5.47280.3111370.2352654X-RAY DIFFRACTION88
5.4728-6.25810.29891500.24092785X-RAY DIFFRACTION94
6.2581-7.85960.27741500.27322871X-RAY DIFFRACTION95
7.8596-29.44410.21781540.20932802X-RAY DIFFRACTION93

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