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- PDB-5i74: X-ray structure of the ts3 human serotonin transporter complexed ... -

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Basic information

Entry
Database: PDB / ID: 5i74
TitleX-ray structure of the ts3 human serotonin transporter complexed with Br-citalopram 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 / serotonergic synapse / positive regulation of serotonin secretion / cocaine binding / serotonin:sodium:chloride symporter activity / sperm ejaculation / neurotransmitter transmembrane transporter activity / negative regulation of synaptic transmission, dopaminergic ...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 / serotonin:sodium:chloride symporter activity / sperm ejaculation / neurotransmitter transmembrane transporter activity / negative regulation of synaptic transmission, dopaminergic / monoamine transmembrane transporter activity / serotonin uptake / monoamine transport / enteric nervous system development / negative regulation of organ growth / cellular response to cGMP / sodium ion binding / serotonin binding / neurotransmitter transport / vasoconstriction / brain morphogenesis / antiporter activity / syntaxin-1 binding / nitric-oxide synthase binding / social behavior / membrane depolarization / sodium ion transmembrane transport / negative regulation of neuron differentiation / endomembrane system / positive regulation of cell cycle / cellular response to retinoic acid / monoatomic cation channel activity / response to nutrient / memory / response to toxic substance / platelet aggregation / circadian rhythm / actin filament binding / integrin binding / response to estradiol / presynaptic membrane / postsynaptic membrane / response to hypoxia / endosome membrane / neuron projection / response to xenobiotic stimulus / membrane raft / 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
Chem-69D / CHOLESTEROL / DODECANE / HEXANE / Sodium-dependent serotonin transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.395 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_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)110,5679
Polymers109,0963
Non-polymers1,4716
Water0
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)110,5679
Polymers109,0963
Non-polymers1,4716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6960 Å2
ΔGint-13 kcal/mol
Surface area41120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.590, 164.000, 140.170
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, 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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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
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
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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

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Non-polymers , 4 types, 4 molecules

#4: Chemical ChemComp-69D / (1S)-1-(4-bromophenyl)-1-[3-(dimethylamino)propyl]-1,3-dihydro-2-benzofuran-5-carbonitrile


Mass: 385.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21BrN2O
#6: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#7: Chemical ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#8: Chemical ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14

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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: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris pH 8.5, 125 mM NaCl, 125 mM magnesium chloride, 33.4% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.902 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.902 Å / Relative weight: 1
ReflectionResolution: 3.395→101.68 Å / Num. obs: 41581 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.06051 / Net I/σ(I): 17.6

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Processing

Software
NameVersionClassification
PHENIXdev_1634refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.395→101.678 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 34.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2962 1980 5 %
Rwork0.2489 --
obs0.251 39603 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.395→101.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7512 0 98 0 7610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077837
X-RAY DIFFRACTIONf_angle_d1.00510693
X-RAY DIFFRACTIONf_dihedral_angle_d10.6892676
X-RAY DIFFRACTIONf_chiral_restr0.2161209
X-RAY DIFFRACTIONf_plane_restr0.0031317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3948-3.47970.44981340.38532544X-RAY DIFFRACTION93
3.4797-3.57380.40331410.35072655X-RAY DIFFRACTION99
3.5738-3.6790.3741390.33162680X-RAY DIFFRACTION99
3.679-3.79770.32921410.29182723X-RAY DIFFRACTION100
3.7977-3.93350.29651420.26352674X-RAY DIFFRACTION100
3.9335-4.0910.3481470.25852710X-RAY DIFFRACTION100
4.091-4.27710.26081370.22142703X-RAY DIFFRACTION100
4.2771-4.50260.28371470.19732705X-RAY DIFFRACTION100
4.5026-4.78470.31531400.18752702X-RAY DIFFRACTION100
4.7847-5.15420.23621480.19512719X-RAY DIFFRACTION100
5.1542-5.67280.2851380.22512697X-RAY DIFFRACTION100
5.6728-6.49360.361410.2472717X-RAY DIFFRACTION100
6.4936-8.18070.29351410.26632691X-RAY DIFFRACTION100
8.1807-101.72350.26971440.25512703X-RAY DIFFRACTION99
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)
13.4451.6087-0.39035.5808-1.92642.9971-0.2977-0.9492-0.29520.5578-0.0607-1.7283-0.6292-0.19290.28041.19790.0229-0.24991.25260.17251.096454.7581167.734852.8472
23.95521.1124-1.68031.50720.86722.2219-0.5072-0.1473-0.4829-2.26080.23440.0930.75941.57210.59713.3294-1.2140.70233.2489-0.6762.334523.9917159.388745.3075
34.31.2111-1.92624.6069-1.38184.43660.15291.29290.83290.53330.10141.8679-0.4854-1.7015-0.11491.68410.5412-0.34671.6235-0.34321.800144.8634187.415953.6391
41.24950.8487-0.02773.7077-1.56840.7311-0.5716-0.506-2.6481-0.29720.37422.7441.3743-3.9366-1.06461.6458-1.13640.93325.9428-0.79653.794213.5896166.575755.1462
52.95410.4191.79091.358-0.27223.3384-0.5507-0.43840.48690.0473-0.08320.1017-0.7964-0.40070.52591.07320.3276-0.25761.37790.03551.198736.852186.28482.9308
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 74:615)

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