+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-8943 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM Structure of the wild-type human serotonin transporter in complex with ibogaine and 15B8 Fab in the inward conformation | |||||||||
マップデータ | Wild-type SERT bound to Fab and in complex with ibogaine in the occluded and inward conformations | |||||||||
試料 |
| |||||||||
機能・相同性 | 機能・相同性情報 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 / negative regulation of synaptic transmission, dopaminergic / sperm ejaculation / enteric nervous system development ...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 / negative regulation of synaptic transmission, dopaminergic / sperm ejaculation / enteric nervous system development / serotonin uptake / cellular response to cGMP / negative regulation of organ growth / sodium ion binding / neurotransmitter transmembrane transporter activity / conditioned place preference / monoamine transmembrane transporter activity / monoamine transport / serotonin binding / vasoconstriction / brain morphogenesis / neurotransmitter transport / antiporter activity / syntaxin-1 binding / amino acid transport / nitric-oxide synthase binding / membrane depolarization / behavioral response to cocaine / social behavior / negative regulation of neuron differentiation / sodium ion transmembrane transport / endomembrane system / monoatomic cation channel activity / positive regulation of cell cycle / response to nutrient / cellular response to retinoic acid / circadian rhythm / response to toxic substance / memory / platelet aggregation / actin filament binding / integrin binding / response to estradiol / presynaptic membrane / postsynaptic membrane / endosome membrane / response to hypoxia / neuron projection / response to xenobiotic stimulus / membrane raft / focal adhesion / synapse / positive regulation of gene expression / identical protein binding / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Mus musculus (ハツカネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.6 Å | |||||||||
データ登録者 | Yang D / Coleman JA / Gouaux E | |||||||||
資金援助 | 米国, 2件
| |||||||||
引用 | ジャーナル: Nature / 年: 2019 タイトル: Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport. 著者: Jonathan A Coleman / Dongxue Yang / Zhiyu Zhao / Po-Chao Wen / Craig Yoshioka / Emad Tajkhorshid / Eric Gouaux / 要旨: The serotonin transporter (SERT) regulates neurotransmitter homeostasis through the sodium- and chloride-dependent recycling of serotonin into presynaptic neurons. Major depression and anxiety ...The serotonin transporter (SERT) regulates neurotransmitter homeostasis through the sodium- and chloride-dependent recycling of serotonin into presynaptic neurons. Major depression and anxiety disorders are treated using selective serotonin reuptake inhibitors-small molecules that competitively block substrate binding and thereby prolong neurotransmitter action. The dopamine and noradrenaline transporters, together with SERT, are members of the neurotransmitter sodium symporter (NSS) family. The transport activities of NSSs can be inhibited or modulated by cocaine and amphetamines, and genetic variants of NSSs are associated with several neuropsychiatric disorders including attention deficit hyperactivity disorder, autism and bipolar disorder. Studies of bacterial NSS homologues-including LeuT-have shown how their transmembrane helices (TMs) undergo conformational changes during the transport cycle, exposing a central binding site to either side of the membrane. However, the conformational changes associated with transport in NSSs remain unknown. To elucidate structure-based mechanisms for transport in SERT we investigated its complexes with ibogaine, a hallucinogenic natural product with psychoactive and anti-addictive properties. Notably, ibogaine is a non-competitive inhibitor of transport but displays competitive binding towards selective serotonin reuptake inhibitors. Here we report cryo-electron microscopy structures of SERT-ibogaine complexes captured in outward-open, occluded and inward-open conformations. Ibogaine binds to the central binding site, and closure of the extracellular gate largely involves movements of TMs 1b and 6a. Opening of the intracellular gate involves a hinge-like movement of TM1a and the partial unwinding of TM5, which together create a permeation pathway that enables substrate and ion diffusion to the cytoplasm. These structures define the structural rearrangements that occur from the outward-open to inward-open conformations, and provide insight into the mechanism of neurotransmitter transport and ibogaine inhibition. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_8943.map.gz | 194.3 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-8943-v30.xml emd-8943.xml | 37.2 KB 37.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_8943_fsc.xml | 14.4 KB | 表示 | FSCデータファイル |
画像 | emd_8943.png | 672.7 KB | ||
マスクデータ | emd_8943_msk_1.map emd_8943_msk_2.map | 209.3 MB 209.3 MB | マスクマップ | |
その他 | emd_8943_additional_1.map.gz emd_8943_additional_2.map.gz emd_8943_additional_3.map.gz emd_8943_additional_4.map.gz emd_8943_additional_5.map.gz emd_8943_additional_6.map.gz emd_8943_additional_7.map.gz emd_8943_additional_8.map.gz emd_8943_additional_9.map.gz emd_8943_half_map_1.map.gz emd_8943_half_map_2.map.gz | 116.1 MB 115.6 MB 11.5 MB 11.5 MB 115.8 MB 115.7 MB 115.1 MB 194.3 MB 191.2 MB 23.4 MB 23.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-8943 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8943 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_8943_validation.pdf.gz | 761 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_8943_full_validation.pdf.gz | 760.5 KB | 表示 | |
XML形式データ | emd_8943_validation.xml.gz | 21.3 KB | 表示 | |
CIF形式データ | emd_8943_validation.cif.gz | 27.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8943 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8943 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_8943.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Wild-type SERT bound to Fab and in complex with ibogaine in the occluded and inward conformations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.823 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
+マスク #1
+マスク #2
+追加マップ: Unsharpened map, data set 2
+追加マップ: Unsharpened map, data set 1
+追加マップ: half map 2, data set 2
+追加マップ: half map 1, data set 2
+追加マップ: Inward class, data set 1
+追加マップ: Occluded class, data set 1
+追加マップ: Unsharpened, aligned and averaged map from data set 1 and 2
+追加マップ: inward class, low resolution
+追加マップ: inward class, unsharpened map
+ハーフマップ: Half map 2, data set 1
+ハーフマップ: Half map 1, data set 1
-試料の構成要素
-全体 : Human serotonin transporter in complex with Fab bound to ibogaine
全体 | 名称: Human serotonin transporter in complex with Fab bound to ibogaine |
---|---|
要素 |
|
-超分子 #1: Human serotonin transporter in complex with Fab bound to ibogaine
超分子 | 名称: Human serotonin transporter in complex with Fab bound to ibogaine タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#3 |
---|
-超分子 #2: serotonin transporter
超分子 | 名称: serotonin transporter / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1 |
---|---|
由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) |
-超分子 #3: 15B8 Fab
超分子 | 名称: 15B8 Fab / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #2-#3 |
---|---|
由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
組換発現 | 生物種: Mus musculus (ハツカネズミ) |
-分子 #1: Sodium-dependent serotonin transporter
分子 | 名称: Sodium-dependent serotonin transporter / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 61.005074 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: ERETWGKKVD FLLSVIGYAV DLGNVWRFPY ICYQNGGGAF LLPYTIMAIF GGIPLFYMEL ALGQYHRNGC ISIWRKICPI FKGIGYAIC IIAFYIASYY NTIMAWALYY LISSFTDQLP WTSCKNSWNT GNCTNYFSED NITWTLHSTS PAEEFYTRHV L QIHRSKGL ...文字列: ERETWGKKVD FLLSVIGYAV DLGNVWRFPY ICYQNGGGAF LLPYTIMAIF GGIPLFYMEL ALGQYHRNGC ISIWRKICPI FKGIGYAIC IIAFYIASYY NTIMAWALYY LISSFTDQLP WTSCKNSWNT GNCTNYFSED NITWTLHSTS PAEEFYTRHV L QIHRSKGL QDLGGISWQL ALCIMLIFTV IYFSIWKGVK TSGKVVWVTA TFPYIILSVL LVRGATLPGA WRGVLFYLKP NW QKLLETG VWIDAAAQIF FSLGPGFGVL LAFASYNKFN NNCYQDALVT SVVNCMTSFV SGFVIFTVLG YMAEMRNEDV SEV AKDAGP SLLFITYAEA IANMPASTFF AIIFFLMLIT LGLDSTFAGL EGVITAVLDE FPHVWAKRRE RFVLAVVITC FFGS LVTLT FGGAYVVKLL EEYATGPAVL TVALIEAVAV SWFYGITQFC RDVKEMLGFS PGWFWRICWV AISPLFLLFI ICSFL MSPP QLRLFQYNYP YWSIILGYCI GTSSFICIPT YIAYRLIITP GTFKERIIKS ITPETP |
-分子 #2: 15B8 antibody heavy chain
分子 | 名称: 15B8 antibody heavy chain / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 12.980533 KDa |
組換発現 | 生物種: Mus musculus (ハツカネズミ) |
配列 | 文字列: QVQLQQSGPE LVKLGASVRI SCKASGYRFS YSWMNWVKQR PGKGLEWIGR IYPGDGDTKY SGKFKGKATL TADKSSSTVY MQLSSLTSE DSAVYFCARS AYGSEGFAMD YWGQGTSVT |
-分子 #3: 15B8 antibody light chain
分子 | 名称: 15B8 antibody light chain / タイプ: protein_or_peptide / ID: 3 / コピー数: 1 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 11.776065 KDa |
組換発現 | 生物種: Mus musculus (ハツカネズミ) |
配列 | 文字列: DIVLTQSPAS LAVSLGQRAT ISCRASESVD NYGISFLNWF QQKPGQPPKL LIYAASNQGS GVPARFSGSG SGTYFSLNIH PMEEDDTAV YFCQQTKGVS WTFGGGTKVE I |
-分子 #5: (5beta)-12-methoxyibogamine
分子 | 名称: (5beta)-12-methoxyibogamine / タイプ: ligand / ID: 5 / コピー数: 1 / 式: HJM |
---|---|
分子量 | 理論値: 310.433 Da |
Chemical component information | ChemComp-HJM: |
-分子 #6: DODECYL-BETA-D-MALTOSIDE
分子 | 名称: DODECYL-BETA-D-MALTOSIDE / タイプ: ligand / ID: 6 / コピー数: 1 / 式: LMT |
---|---|
分子量 | 理論値: 510.615 Da |
Chemical component information | ChemComp-LMT: |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 8 |
---|---|
グリッド | 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |