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- PDB-5i6z: X-ray structure of the ts2 human serotonin transporter -

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Basic information

Entry
Database: PDB / ID: 5i6z
TitleX-ray structure of the ts2 human serotonin transporter
Components
  • 8B6 antibody, heavy chain
  • 8B6 antibody, light chain
  • 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 / cocaine binding / negative regulation of synaptic transmission, dopaminergic / 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 / cocaine binding / negative regulation of synaptic transmission, dopaminergic / serotonin:sodium:chloride symporter activity / cellular response to cGMP / enteric nervous system development / sodium ion binding / negative regulation of organ growth / neurotransmitter transmembrane transporter activity / serotonin uptake / monoamine transmembrane transporter activity / monoamine transport / serotonin binding / conditioned place preference / vasoconstriction / brain morphogenesis / syntaxin-1 binding / antiporter activity / neurotransmitter transport / nitric-oxide synthase binding / male mating behavior / amino acid transport / behavioral response to cocaine / membrane depolarization / negative regulation of neuron differentiation / monoatomic cation channel activity / cellular response to retinoic acid / positive regulation of cell cycle / response to nutrient / sodium ion transmembrane transport / endomembrane system / memory / platelet aggregation / response to toxic substance / circadian rhythm / actin filament binding / integrin 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.
Similarity search - Domain/homology
Sodium-dependent serotonin transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.53 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
Revision 1.5Nov 20, 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)109,4104
Polymers109,1883
Non-polymers2211
Water00
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)109,4104
Polymers109,1883
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+5/21
Buried area5480 Å2
ΔGint-24 kcal/mol
Surface area41140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.750, 162.810, 140.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 61781.859 Da / Num. of mol.: 1 / Mutation: 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
#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)
#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.: 1
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
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: 63.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris pH 8, 250 mM LiCl, 34.7% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.53→40.5 Å / Num. obs: 17307 / % possible obs: 99.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.186 / Net I/σ(I): 8.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.53→40.5 Å / SU ML: 0.85 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 43.14
RfactorNum. reflection% reflection
Rfree0.317 822 4.99 %
Rwork0.28 --
obs0.282 16485 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.53→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7530 0 14 0 7544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027768
X-RAY DIFFRACTIONf_angle_d0.49810610
X-RAY DIFFRACTIONf_dihedral_angle_d12.0574482
X-RAY DIFFRACTIONf_chiral_restr0.0381197
X-RAY DIFFRACTIONf_plane_restr0.0031317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5315-4.8150.3641310.3832516X-RAY DIFFRACTION96
4.815-5.1860.39441380.35322639X-RAY DIFFRACTION100
5.186-5.70660.39311390.34132618X-RAY DIFFRACTION100
5.7066-6.52940.44761350.35782639X-RAY DIFFRACTION100
6.5294-8.21510.33371380.30142635X-RAY DIFFRACTION100
8.2151-40.50060.26031410.22822616X-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)
14.69422.8136-7.56142.0795-4.21482.08591.2393-0.88530.611.0779-2.9491-6.8388-6.86790.4945-0.5093.79490.9086-0.3952.65290.28882.609654.8766166.7648193.0625
24.0623-0.2535-2.37861.0147-0.33483.70580.4208-1.853-1.2590.0095-1.10361.47121.10860.4103-0.01512.73620.17352.62032.521-3.14940.495824.1844158.2189185.4012
33.92454.6393-4.09912.05561.95338.75933.26590.2561.95694.13413.69231.5381-2.11070.192128.86772.31930.4961-0.40442.317-1.60372.6644.7185186.2566193.5817
42.28680.06270.27416.96821.65355.7535-1.27270.08290.4383-2.8104-1.5857-0.4193-0.4675-6.173-0.97792.9444-0.5292-0.47065.9057-0.533.539513.6598165.1961194.9762
52.24780.8164.10920.3624-2.22392.6438-1.5046-0.3867-0.89130.3180.1247-1.38630.84710.0189-3.19382.16080.1755-0.45872.4343-0.29083.004336.8755185.0157142.8382
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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