[English] 日本語
Yorodumi
- PDB-5i74: X-ray structure of the ts3 human serotonin transporter complexed ... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / antiporter activity / syntaxin-1 binding / male mating behavior / negative regulation of neuron differentiation / 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
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
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)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

-
Components

-
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)

-
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-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

-
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


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


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


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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more