+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-30341 | |||||||||
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タイトル | Consensus mutated xCT-CD98hc complex | |||||||||
マップデータ | Main map | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 cystine:glutamate antiporter activity / regulation of neutrophil apoptotic process / L-kynurenine transmembrane transport / L-kynurenine transmembrane transporter activity / regulation of cysteine metabolic process / regulation of glutathione biosynthetic process / regulation of glutamate metabolic process / regulation of melanin biosynthetic process / regulation of AMPA glutamate receptor clustering / L-cystine transport ...cystine:glutamate antiporter activity / regulation of neutrophil apoptotic process / L-kynurenine transmembrane transport / L-kynurenine transmembrane transporter activity / regulation of cysteine metabolic process / regulation of glutathione biosynthetic process / regulation of glutamate metabolic process / regulation of melanin biosynthetic process / regulation of AMPA glutamate receptor clustering / L-cystine transport / neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / methionine transport / tyrosine transport / L-histidine transport / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / L-amino acid transmembrane transporter activity / dipeptide import across plasma membrane / : / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / isoleucine transport / L-alanine import across plasma membrane / regulation of protein transport / phenylalanine transport / valine transport / L-leucine transmembrane transporter activity / amino acid transmembrane transport / negative regulation of ferroptosis / calcium:sodium antiporter activity / L-leucine transport / thyroid hormone transport / proline transport / L-glutamate transmembrane transport / glutathione transmembrane transport / regulation of cellular response to oxidative stress / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / ventricular system development / intracellular glutamate homeostasis / lens fiber cell differentiation / L-glutamate import across plasma membrane / Tryptophan catabolism / striatum development / astrocyte projection / exogenous protein binding / anchoring junction / limb development / Basigin interactions / response to redox state / NFE2L2 regulating anti-oxidant/detoxification enzymes / microvillus membrane / adult behavior / amino acid transport / regulation of synapse organization / lung alveolus development / response to exogenous dsRNA / tryptophan transport / glutathione metabolic process / basal plasma membrane / brush border membrane / response to nicotine / visual learning / modulation of chemical synaptic transmission / response to organic cyclic compound / response to toxic substance / platelet aggregation / calcium ion transport / double-stranded RNA binding / melanosome / apical part of cell / virus receptor activity / regulation of cell population proliferation / cellular response to oxidative stress / basolateral plasma membrane / carbohydrate metabolic process / cadherin binding / symbiont entry into host cell / apical plasma membrane / protein heterodimerization activity / lysosomal membrane / synapse / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / nucleoplasm / membrane / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.2 Å | |||||||||
データ登録者 | Oda K / Lee Y / Takemoto M / Yamashita K / Nishizawa T / Nureki O | |||||||||
引用 | ジャーナル: Protein Sci / 年: 2020 タイトル: Consensus mutagenesis approach improves the thermal stability of system x transporter, xCT, and enables cryo-EM analyses. 著者: Kazumasa Oda / Yongchan Lee / Pattama Wiriyasermkul / Yoko Tanaka / Mizuki Takemoto / Keitaro Yamashita / Shushi Nagamori / Tomohiro Nishizawa / Osamu Nureki / 要旨: System x is an amino acid antiporter that imports L-cystine into cells and exports intracellular L-glutamate, at a 1:1 ratio. As L-cystine is an essential precursor for glutathione synthesis, system ...System x is an amino acid antiporter that imports L-cystine into cells and exports intracellular L-glutamate, at a 1:1 ratio. As L-cystine is an essential precursor for glutathione synthesis, system x supports tumor cell growth through glutathione-based oxidative stress resistance and is considered as a potential therapeutic target for cancer treatment. System x consists of two subunits, the light chain subunit SLC7A11 (xCT) and the heavy chain subunit SLC3A2 (also known as CD98hc or 4F2hc), which are linked by a conserved disulfide bridge. Although the recent structures of another SLC7 member, L-type amino acid transporter 1 (LAT1) in complex with CD98hc, have provided the structural basis toward understanding the amino acid transport mechanism, the detailed molecular mechanism of xCT remains unknown. To revealthe molecular mechanism, we performed single-particle analyses of the xCT-CD98hc complex. As wild-type xCT-CD98hc displayed poor stability and could not be purified to homogeneity, we applied a consensus mutagenesis approach to xCT. The consensus mutated construct exhibited increased stability as compared to the wild-type, and enabled the cryoelectron microscopy (cryo-EM) map to be obtained at 6.2 Å resolution by single-particle analysis. The cryo-EM map revealed sufficient electron density to assign secondary structures. In the xCT structure, the hash and arm domains are well resolved, whereas the bundle domain shows some flexibility. CD98hc is positioned next to the xCT transmembrane domain. This study provides the structural basis of xCT, and our consensus-based strategy could represent a good choice toward solving unstable protein structures. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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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_30341.map.gz | 4.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-30341-v30.xml emd-30341.xml | 16.3 KB 16.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_30341_fsc.xml | 6.5 KB | 表示 | FSCデータファイル |
画像 | emd_30341.png | 26.8 KB | ||
マスクデータ | emd_30341_msk_1.map | 22.2 MB | マスクマップ | |
その他 | emd_30341_half_map_1.map.gz emd_30341_half_map_2.map.gz | 16.7 MB 16.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-30341 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30341 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_30341_validation.pdf.gz | 566.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_30341_full_validation.pdf.gz | 566.4 KB | 表示 | |
XML形式データ | emd_30341_validation.xml.gz | 11.9 KB | 表示 | |
CIF形式データ | emd_30341_validation.cif.gz | 16.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30341 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30341 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「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_30341.map.gz / 形式: CCP4 / 大きさ: 22.2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Main map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.47556 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-マスク #1
ファイル | emd_30341_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half2
ファイル | emd_30341_half_map_1.map | ||||||||||||
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注釈 | Half2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half1
ファイル | emd_30341_half_map_2.map | ||||||||||||
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注釈 | Half1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Consensus mutated xCT-CD98hc complex
全体 | 名称: Consensus mutated xCT-CD98hc complex |
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要素 |
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-超分子 #1: Consensus mutated xCT-CD98hc complex
超分子 | 名称: Consensus mutated xCT-CD98hc complex / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) |
分子量 | 実験値: 120 KDa |
-分子 #1: 4F2 cell-surface antigen heavy chain
分子 | 名称: 4F2 cell-surface antigen heavy chain / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 68.069625 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: GSELQPPEAS IAVVSIPRQL PGSHSEAGVQ GLSAGDDSEL GSHCVAQTGL ELLASGDPLP SASQNAEMIE TGSDCVTQAG LQLLASSDP PALASKNAEV TGTMSQDTEV DMKEVELNEL EPEKQPMNAA SGAAMSLAGA EKNGLVKIKV AEDEAEAAAA A KFTGLSKE ...文字列: GSELQPPEAS IAVVSIPRQL PGSHSEAGVQ GLSAGDDSEL GSHCVAQTGL ELLASGDPLP SASQNAEMIE TGSDCVTQAG LQLLASSDP PALASKNAEV TGTMSQDTEV DMKEVELNEL EPEKQPMNAA SGAAMSLAGA EKNGLVKIKV AEDEAEAAAA A KFTGLSKE ELLKVAGSPG WVRTRWALLL LFWLGWLGML AGAVVIIVRA PRCRELPAQK WWHTGALYRI GDLQAFQGHG AG NLAGLKG RLDYLSSLKV KGLVLGPIHK NQKDDVAQTD LLQIDPNFGS KEDFDSLLQS AKKKSIRVIL DLTPNYRGEN SWF STQVDT VATKVKDALE FWLQAGVDGF QVRDIENLKD ASSFLAEWQN ITKGFSEDRL LIAGTNSSDL QQILSLLESN KDLL LTSSY LSDSGSTGEH TKSLVTQYLN ATGNRWCSWS LSQARLLTSF LPAQLLRLYQ LMLFTLPGTP VFSYGDEIGL DAAAL PGQP MEAPVMLWDE SSFPDIPGAV SANMTVKGQS EDPGSLLSLF RRLSDQRSKE RSLLHGDFHA FSAGPGLFSY IRHWDQ NER FLVVLNFGDV GLSAGLQASD LPASASLPAK ADLLLSTQPG REEGSPLELE RLKLEPHEGL LLRFPYAA |
-分子 #2: Consensus mutated Anionic Amino Acid Transporter Light Chain, Xc-...
分子 | 名称: Consensus mutated Anionic Amino Acid Transporter Light Chain, Xc- System タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 55.933852 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MVRKPVVSTI SKGGYLQGNV NGRLPSLGSK EPPGQEKVQL KREITLLDGV SLIVGTIIGA GIFVSPKGVL KNTGSVGLSL VIWAVCGVL SLFGALCYAE LGTTIPKSGG AYLYILETFG PLPAFLRGWN ELLIIRPAST AVISLAFGNY ILEPFFPTCE P PELAIKLL ...文字列: MVRKPVVSTI SKGGYLQGNV NGRLPSLGSK EPPGQEKVQL KREITLLDGV SLIVGTIIGA GIFVSPKGVL KNTGSVGLSL VIWAVCGVL SLFGALCYAE LGTTIPKSGG AYLYILETFG PLPAFLRGWN ELLIIRPAST AVISLAFGNY ILEPFFPTCE P PELAIKLL AAVGILLLTV LNSLSVKWSA RVQDFFTAAK LLALLIIIVP GVVQLIKGQT QNFKDAFEGS DPSIGGLPLA FY SGLYAYV GWDYLNFVTE EVKNPEKNIP LAIVISMPIV TVAYVLTNVA YFTTLSPEEL LLSNAVAVTF GERLLGNFSW AVP IFVALS CFGSLNGSLF AMSRLFYVAA REGHLPKILS MIHVRRHTPL PALIVSGPLT AIMLFLGDLF SLINFMSFGT WLFY GLVVA GLIYLRYKKP DLHRPIKVPL FIPILFLLTC LFLVAVSLYS DPVNCGIGFV IILTGVPVYF LFVYWDKKPK WFRRI SEKI TRHLQLLLEV VPEEDKLDYK DDDDK |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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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 |
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER/RHODIUM / メッシュ: 300 / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 49.76 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 |