+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9849 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | LAT1-CD98hc complex bound to MEM-108 Fab | |||||||||
マップデータ | Sharpened, masked map | |||||||||
試料 |
| |||||||||
機能・相同性 | 機能・相同性情報 L-tryptophan transmembrane transporter activity / alanine transport / L-tryptophan transmembrane transport / positive regulation of L-leucine import across plasma membrane / cellular response to L-arginine / amino acid import across plasma membrane / thyroid hormone transmembrane transporter activity / neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / tyrosine transport ...L-tryptophan transmembrane transporter activity / alanine transport / L-tryptophan transmembrane transport / positive regulation of L-leucine import across plasma membrane / cellular response to L-arginine / amino acid import across plasma membrane / thyroid hormone transmembrane transporter activity / neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / 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 / methionine transport / : / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / isoleucine transport / L-alanine import across plasma membrane / phenylalanine transport / valine transport / L-leucine transmembrane transporter activity / proline transport / amino acid transmembrane transport / positive regulation of cytokine production involved in immune response / calcium:sodium antiporter activity / L-leucine transport / thyroid hormone transport / neutral amino acid transport / negative regulation of vascular associated smooth muscle cell apoptotic process / amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / external side of apical plasma membrane / Tryptophan catabolism / exogenous protein binding / amino acid transport / xenobiotic transport / anchoring junction / antiporter activity / response to muscle activity / Basigin interactions / microvillus membrane / response to exogenous dsRNA / positive regulation of interleukin-17 production / tryptophan transport / transport across blood-brain barrier / positive regulation of interleukin-4 production / response to hyperoxia / cellular response to glucose starvation / positive regulation of glial cell proliferation / basal plasma membrane / negative regulation of autophagy / liver regeneration / peptide antigen binding / calcium ion transport / positive regulation of type II interferon production / メラノソーム / double-stranded RNA binding / virus receptor activity / basolateral plasma membrane / cellular response to lipopolysaccharide / carbohydrate metabolic process / cadherin binding / symbiont entry into host cell / apical plasma membrane / protein heterodimerization activity / lysosomal membrane / negative regulation of gene expression / intracellular membrane-bounded organelle / シナプス / 細胞膜 / protein homodimerization activity / RNA binding / extracellular exosome / 核質 / 生体膜 / 細胞膜 / 細胞質基質 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: 3.31 Å | |||||||||
データ登録者 | Lee Y / Nishizawa T / Kusakizako T / Oda K / Ishitani R / Nakane T / Nureki O | |||||||||
資金援助 | 日本, 2件
| |||||||||
引用 | ジャーナル: Nat Struct Mol Biol / 年: 2019 タイトル: Cryo-EM structure of the human L-type amino acid transporter 1 in complex with glycoprotein CD98hc. 著者: Yongchan Lee / Pattama Wiriyasermkul / Chunhuan Jin / Lili Quan / Ryuichi Ohgaki / Suguru Okuda / Tsukasa Kusakizako / Tomohiro Nishizawa / Kazumasa Oda / Ryuichiro Ishitani / Takeshi ...著者: Yongchan Lee / Pattama Wiriyasermkul / Chunhuan Jin / Lili Quan / Ryuichi Ohgaki / Suguru Okuda / Tsukasa Kusakizako / Tomohiro Nishizawa / Kazumasa Oda / Ryuichiro Ishitani / Takeshi Yokoyama / Takanori Nakane / Mikako Shirouzu / Hitoshi Endou / Shushi Nagamori / Yoshikatsu Kanai / Osamu Nureki / 要旨: The L-type amino acid transporter 1 (LAT1 or SLC7A5) transports large neutral amino acids across the membrane and is crucial for brain drug delivery and tumor growth. LAT1 forms a disulfide-linked ...The L-type amino acid transporter 1 (LAT1 or SLC7A5) transports large neutral amino acids across the membrane and is crucial for brain drug delivery and tumor growth. LAT1 forms a disulfide-linked heterodimer with CD98 heavy chain (CD98hc, 4F2hc or SLC3A2), but the mechanism of assembly and amino acid transport are poorly understood. Here we report the cryo-EM structure of the human LAT1-CD98hc heterodimer at 3.3-Å resolution. LAT1 features a canonical Leu T-fold and exhibits an unusual loop structure on transmembrane helix 6, creating an extended cavity that might accommodate bulky amino acids and drugs. CD98hc engages with LAT1 through the extracellular, transmembrane and putative cholesterol-mediated interactions. We also show that two anti-CD98 antibodies recognize distinct, multiple epitopes on CD98hc but not its glycans, explaining their robust reactivities. These results reveal the principles of glycoprotein-solute carrier assembly and provide templates for improving preclinical drugs and antibodies targeting LAT1 or CD98hc. | |||||||||
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_9849.map.gz | 5.5 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-9849-v30.xml emd-9849.xml | 21.9 KB 21.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_9849_fsc.xml | 10.2 KB | 表示 | FSCデータファイル |
画像 | emd_9849.png | 94.1 KB | ||
マスクデータ | emd_9849_msk_1.map | 91.1 MB | マスクマップ | |
その他 | emd_9849_half_map_1.map.gz emd_9849_half_map_2.map.gz | 71.3 MB 71.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9849 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9849 | HTTPS FTP |
-関連構造データ
関連構造データ | 6jmqMC 9850C 6jmrC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
---|---|
類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10264 (タイトル: LAT1-CD98hc bound to MEM-108 Fab / Data size: 4.1 TB Data #1: Unaligned multi-frame micrographs, Dataset1 [micrographs - multiframe] Data #2: Unaligned multi-frame micrographs, Dataset2 [micrographs - multiframe] Data #3: Micelle subtracted particles used for final reconstruction [picked particles - single frame - processed]) |
-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_9849.map.gz / 形式: CCP4 / 大きさ: 91.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Sharpened, masked map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.333 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
ファイル | emd_9849_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: Half map 2 used for FSC calculation. The...
ファイル | emd_9849_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Half map 2 used for FSC calculation. The header contains a wrong pixel size information (1.375 A). The correct pixel size is 1.333 A. | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: Half map 1 used for FSC calculation. The...
ファイル | emd_9849_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Half map 1 used for FSC calculation. The header contains a wrong pixel size information (1.375 A). The correct pixel size is 1.333 A. | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
-全体 : LAT1-CD98hc complex bound to MEM-108 Fab
全体 | 名称: LAT1-CD98hc complex bound to MEM-108 Fab |
---|---|
要素 |
|
-超分子 #1: LAT1-CD98hc complex bound to MEM-108 Fab
超分子 | 名称: LAT1-CD98hc complex bound to MEM-108 Fab / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#4 |
---|---|
由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 実験値: 175 kDa/nm |
-分子 #1: Large neutral amino acids transporter small subunit 1
分子 | 名称: Large neutral amino acids transporter small subunit 1 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: 56.043746 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MAGAGPKRRA LAAPAAEEKE EAREKMLAAK SADGSAPAGE GEGVTLQRNI TLLNGVAIIV GTIIGSGIFV TPTGVLKEAG SPGLALVVW AACGVFSIVG ALCYAELGTT ISKSGGDYAY MLEVYGSLPA FLKLWIELLI IRPSSQYIVA LVFATYLLKP L FPTCPVPE ...文字列: MAGAGPKRRA LAAPAAEEKE EAREKMLAAK SADGSAPAGE GEGVTLQRNI TLLNGVAIIV GTIIGSGIFV TPTGVLKEAG SPGLALVVW AACGVFSIVG ALCYAELGTT ISKSGGDYAY MLEVYGSLPA FLKLWIELLI IRPSSQYIVA LVFATYLLKP L FPTCPVPE EAAKLVACLC VLLLTAVNCY SVKAATRVQD AFAAAKLLAL ALIILLGFVQ IGKGDVSNLD PNFSFEGTKL DV GNIVLAL YSGLFAYGGW NYLNFVTEEM INPYRNLPLA IIISLPIVTL VYVLTNLAYF TTLSTEQMLS SEAVAVDFGN YHL GVMSWI IPVFVGLSCF GSVNGSLFTS SRLFFVGSRE GHLPSILSMI HPQLLTPVPS LVFTCVMTLL YAFSKDIFSV INFF SFFNW LCVALAIIGM IWLRHRKPEL ERPIKVNLAL PVFFILACLF LIAVSFWKTP VECGIGFTII LSGLPVYFFG VWWKN KPKW LLQGIFSTTV LCQKLMQVVP QETDYKDDDD K |
-分子 #2: 4F2 cell-surface antigen heavy chain
分子 | 名称: 4F2 cell-surface antigen 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: 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 #3: Antibody
分子 | 名称: Antibody / 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: 22.577857 KDa |
組換発現 | 生物種: Mus musculus (ハツカネズミ) |
配列 | 文字列: QVQLKESGPG LVAPSQSLSI TCTVSGFPLT (UNK)(UNK)(UNK)(UNK)(UNK)WVRQP PGKGLEWLG(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)RLSI SKDNSK SQV FLKMNSLQTD ...文字列: QVQLKESGPG LVAPSQSLSI TCTVSGFPLT (UNK)(UNK)(UNK)(UNK)(UNK)WVRQP PGKGLEWLG(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)RLSI SKDNSK SQV FLKMNSLQTD DTARYYCAR(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)W GQGTSVT VS SAKTTPPSVY PLAPGS(UNK)(UNK)(UNK)(UNK) (UNK)SMVTLGCLV KGYFPEPVTV TWNSGSLSSG VHTFPAVL Q SDLYTLSSSV TVPSSTWPSE TVTCNVAHPA SSTKVDKKIV PRD |
-分子 #4: Antibody
分子 | 名称: Antibody / タイプ: protein_or_peptide / ID: 4 / 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: 23.227152 KDa |
組換発現 | 生物種: Mus musculus (ハツカネズミ) |
配列 | 文字列: DIVMSQSPSS LVVSVGEKVT MSC(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)WYQQKPGQS PKLLIY(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) GVPDRF TGSGSGTDFT ...文字列: DIVMSQSPSS LVVSVGEKVT MSC(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)WYQQKPGQS PKLLIY(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) GVPDRF TGSGSGTDFT LTISSVKAED LAVYYC(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)FGG G TKLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID GSERQNGVLN SWTDQDSKDS TYSMSSTLT LTKDEYERHN SYTCEATHKT STSPIVKSFN RNE |
-分子 #5: CHOLESTEROL
分子 | 名称: CHOLESTEROL / タイプ: ligand / ID: 5 / コピー数: 5 / 式: CLR |
---|---|
分子量 | 理論値: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-分子 #6: N-ACETYL-D-GLUCOSAMINE
分子 | 名称: N-ACETYL-D-GLUCOSAMINE / タイプ: ligand / ID: 6 / コピー数: 5 / 式: NAG |
---|---|
分子量 | 理論値: 221.208 Da |
-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 |
---|---|
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
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 FIELDBright-field microscopy |
撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 平均電子線量: 7.14 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |