+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-24369 | |||||||||
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タイトル | Cryo-EM Structure of the HCMV gHgLgO Trimer Derived from AD169 and TR strains in complex with PDGFRalpha | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 platelet-derived growth factor alpha-receptor activity / Imatinib-resistant PDGFR mutants / Sunitinib-resistant PDGFR mutants / Regorafenib-resistant PDGFR mutants / Sorafenib-resistant PDGFR mutants / PDGFR mutants bind TKIs / platelet-derived growth factor receptor-alpha signaling pathway / metanephric glomerular capillary formation / regulation of mesenchymal stem cell differentiation / luteinization ...platelet-derived growth factor alpha-receptor activity / Imatinib-resistant PDGFR mutants / Sunitinib-resistant PDGFR mutants / Regorafenib-resistant PDGFR mutants / Sorafenib-resistant PDGFR mutants / PDGFR mutants bind TKIs / platelet-derived growth factor receptor-alpha signaling pathway / metanephric glomerular capillary formation / regulation of mesenchymal stem cell differentiation / luteinization / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / platelet-derived growth factor binding / embryonic digestive tract morphogenesis / embryonic skeletal system morphogenesis / vascular endothelial growth factor binding / retina vasculature development in camera-type eye / cardiac myofibril assembly / vascular endothelial growth factor receptor activity / Leydig cell differentiation / cell activation / male genitalia development / positive regulation of chemotaxis / Signaling by PDGF / signal transduction involved in regulation of gene expression / embryonic cranial skeleton morphogenesis / platelet-derived growth factor receptor binding / face morphogenesis / estrogen metabolic process / adrenal gland development / roof of mouth development / odontogenesis of dentin-containing tooth / microvillus / platelet-derived growth factor receptor signaling pathway / white fat cell differentiation / negative regulation of platelet activation / hematopoietic progenitor cell differentiation / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / transmembrane receptor protein tyrosine kinase activity / positive regulation of calcium-mediated signaling / Downstream signal transduction / extracellular matrix organization / cell chemotaxis / host cell endosome membrane / platelet aggregation / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / membrane => GO:0016020 / lung development / wound healing / receptor protein-tyrosine kinase / cilium / peptidyl-tyrosine phosphorylation / cellular response to reactive oxygen species / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of fibroblast proliferation / PIP3 activates AKT signaling / cell junction / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / host cell Golgi apparatus / in utero embryonic development / protein autophosphorylation / entry receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein kinase activity / positive regulation of cell migration / symbiont entry into host cell / external side of plasma membrane / fusion of virus membrane with host plasma membrane / viral envelope / positive regulation of cell population proliferation / endoplasmic reticulum membrane / protein-containing complex binding / host cell plasma membrane / virion membrane / Golgi apparatus / protein homodimerization activity / protein-containing complex / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Human herpesvirus 5 strain AD169 (ヘルペスウイルス) / Homo sapiens (ヒト) / Human betaherpesvirus 5 (ヘルペスウイルス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.43 Å | |||||||||
データ登録者 | Liu J / Vanarsdall AL / Chen D / Johnson DC / Jardetzky TS | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: mBio / 年: 2021 タイトル: Cryo-Electron Microscopy Structure and Interactions of the Human Cytomegalovirus gHgLgO Trimer with Platelet-Derived Growth Factor Receptor Alpha. 著者: Jing Liu / Adam Vanarsdall / Dong-Hua Chen / Andrea Chin / David Johnson / Theodore S Jardetzky / 要旨: Human cytomegalovirus (HCMV) is a herpesvirus that produces disease in transplant patients and newborn children. Entry of HCMV into cells relies on gH/gL trimer (gHgLgO) and pentamer (gHgLUL128-131) ...Human cytomegalovirus (HCMV) is a herpesvirus that produces disease in transplant patients and newborn children. Entry of HCMV into cells relies on gH/gL trimer (gHgLgO) and pentamer (gHgLUL128-131) complexes that bind cellular receptors. Here, we studied the structure and interactions of the HCMV trimer, formed by AD169 strain gH and gL and TR strain gO proteins, with the human platelet-derived growth factor receptor alpha (PDGFRα). Three trimer surfaces make extensive contacts with three PDGFRα N-terminal domains, causing PDGFRα to wrap around gO in a structure similar to a human hand, explaining the high-affinity interaction. gO is among the least conserved HCMV proteins, with 8 distinct genotypes. We observed high conservation of residues mediating gO-gL interactions but more extensive gO variability in the PDGFRα interface. Comparisons between our trimer structure and a previously determined structure composed of different subunit genotypes indicate that gO variability is accommodated by adjustments in the gO-PDGFRα interface. We identified two loops within gO that were disordered and apparently glycosylated, which could be deleted without disrupting PDGFRα binding. We also identified four gO residues that contact PDGFRα, which when mutated produced markedly reduced receptor binding. These residues fall within conserved contact sites of gO with PDGFRα and may represent key targets for anti-trimer neutralizing antibodies and HCMV vaccines. Finally, we observe that gO mutations distant from the gL interaction site impact trimer expression, suggesting that the intrinsic folding or stability of gO can impact the efficiency of trimer assembly. HCMV is a herpesvirus that infects a large percentage of the adult population and causes significant levels of disease in immunocompromised individuals and birth defects in the developing fetus. The virus encodes a complex protein machinery that coordinates infection of different cell types in the body, including a trimer formed of gH, gL, and gO subunits. Here, we studied the interactions of the HCMV trimer with its receptor on cells, the platelet derived growth factor receptor α (PDGFRα), to better understand how HCMV coordinates virus entry into cells. Our results add to our understanding of HCMV strain-specific differences and identify sites on the trimer that represent potential targets for therapeutic antibodies or vaccine development. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_24369.map.gz | 168.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-24369-v30.xml emd-24369.xml | 26.8 KB 26.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_24369_fsc.xml | 14.4 KB | 表示 | FSCデータファイル |
画像 | emd_24369.png | 85.5 KB | ||
その他 | emd_24369_additional_1.map.gz emd_24369_additional_2.map.gz emd_24369_additional_3.map.gz emd_24369_half_map_1.map.gz emd_24369_half_map_2.map.gz | 168.1 MB 168.1 MB 160.5 MB 165.1 MB 165.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-24369 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24369 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_24369_validation.pdf.gz | 844.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_24369_full_validation.pdf.gz | 844.1 KB | 表示 | |
XML形式データ | emd_24369_validation.xml.gz | 20.7 KB | 表示 | |
CIF形式データ | emd_24369_validation.cif.gz | 26.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24369 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24369 | HTTPS FTP |
-関連構造データ
関連構造データ | 7ramMC 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) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_24369.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: #3
ファイル | emd_24369_additional_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: #2
ファイル | emd_24369_additional_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: #1
ファイル | emd_24369_additional_3.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: #2
ファイル | emd_24369_half_map_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: #1
ファイル | emd_24369_half_map_2.map | ||||||||||||
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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 : HCMV trimer in complex with receptor PDGFRalpha
全体 | 名称: HCMV trimer in complex with receptor PDGFRalpha |
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要素 |
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-超分子 #1: HCMV trimer in complex with receptor PDGFRalpha
超分子 | 名称: HCMV trimer in complex with receptor PDGFRalpha / タイプ: complex / キメラ: Yes / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Human herpesvirus 5 strain AD169 (ヘルペスウイルス) |
組換発現 | 生物種: Homo sapiens (ヒト) |
-超分子 #2: human platelet-derived growth factor receptor alpha extracellular...
超分子 | 名称: human platelet-derived growth factor receptor alpha extracellular domain タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #4 |
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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 #1: Envelope glycoprotein H
分子 | 名称: Envelope glycoprotein H / 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: Human herpesvirus 5 strain AD169 (ヘルペスウイルス) 株: AD169 |
分子量 | 理論値: 80.43543 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: LLLNTYGRPI RFLRENTTQC TYNSSLRNST VVRENAISFN FFQSYNQYYV FHMPRCLFAG PLAEQFLNQV DLTETLERYQ QRLNTYALV SKDLASYRSF SQQLKAQDSL GQQPTTVPPP IDLSIPHVWM PPQTTPHDWK GSHTTSGLHR PHFNQTCILF D GHDLLFST ...文字列: LLLNTYGRPI RFLRENTTQC TYNSSLRNST VVRENAISFN FFQSYNQYYV FHMPRCLFAG PLAEQFLNQV DLTETLERYQ QRLNTYALV SKDLASYRSF SQQLKAQDSL GQQPTTVPPP IDLSIPHVWM PPQTTPHDWK GSHTTSGLHR PHFNQTCILF D GHDLLFST VTPCLHQGFY LMDELRYVKI TLTEDFFVVT VSIDDDTPML LIFGHLPRVL FKAPYQRDNF ILRQTEKHEL LV LVKKAQL NRHSYLKDSD FLDAALDFNY LDLSALLRNS FHRYAVDVLK SGRCQMLDRR TVEMAFAYAL ALFAAARQEE AGT EISIPR ALDRQAALLQ IQEFMITCLS QTPPRTTLLL YPTAVDLAKR ALWTPDQITD ITSLVRLVYI LSKQNQQHLI PQWA LRQIA DFALQLHKTH LASFLSAFAR QELYLMGSLV HSMLVHTTER REIFIVETGL CSLAELSHFT QLLAHPHHEY LSDLY TPCS SSGRRDHSLE RLTRLFPDAT VPATVPAALS ILSTMQPSTL ETFPDLFCLP LGESFSALTV SEHVSYVVTN QYLIKG ISY PVSTTVVGQS LIITQTDSQT KCELTRNMHT THSITAALNI SLENCAFCQS ALLEYDDTQG VINIMYMHDS DDVLFAL DP YNEVVVSSPR THYLMLLKNG TVLEVTDVVV DATDSRGSLV PRGSSAWSHP QFEKAGHHHH HHHH |
-分子 #2: Envelope glycoprotein L
分子 | 名称: Envelope glycoprotein L / 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: Human herpesvirus 5 strain AD169 (ヘルペスウイルス) 株: AD169 |
分子量 | 理論値: 27.138018 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: PTAAEKVPAE CPELTRRCLL GEVFQGDKYE SWLRPLVNVT RRDGPLSQLI RYRPVTPEAA NSVLLDDAFL DTLALLYNNP DQLRALLTL LSSDTAPRWM TVMRGYSECG DGSPAVYTCV DDLCRGYDLT RLSYGRSIFT EHVLGFELVP PSLFNVVVAI R NEATRTNR ...文字列: PTAAEKVPAE CPELTRRCLL GEVFQGDKYE SWLRPLVNVT RRDGPLSQLI RYRPVTPEAA NSVLLDDAFL DTLALLYNNP DQLRALLTL LSSDTAPRWM TVMRGYSECG DGSPAVYTCV DDLCRGYDLT RLSYGRSIFT EHVLGFELVP PSLFNVVVAI R NEATRTNR AVRLPVSTAA APEGITLFYG LYNAVKEFCL RHQLDPPLLR HLDKYYAGLP PELKQTRVNL PAHSRYGPQA VD AR |
-分子 #3: Envelope glycoprotein O
分子 | 名称: Envelope glycoprotein O / タイプ: protein_or_peptide / ID: 3 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Human betaherpesvirus 5 (ヘルペスウイルス) |
分子量 | 理論値: 53.937715 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MGRKGEMRGV FNLFFLMSLT FLLFSFINCR AAVRLSVGRY WSGKVLSTIG KQRLDKFKLE ILKQLEKDIY TKYFNMTRQH IKNLTMNMT EFPRYYILAG PIQNNSVTYL WFDFYSTQLR KPAKYVFSEY NHTAKTITFR PPSCGTVPSM TCLSEMLNVS K RNDTGEQG ...文字列: MGRKGEMRGV FNLFFLMSLT FLLFSFINCR AAVRLSVGRY WSGKVLSTIG KQRLDKFKLE ILKQLEKDIY TKYFNMTRQH IKNLTMNMT EFPRYYILAG PIQNNSVTYL WFDFYSTQLR KPAKYVFSEY NHTAKTITFR PPSCGTVPSM TCLSEMLNVS K RNDTGEQG CGNFTTFNPM FFNVPRWNTK LYVGSKKVNV DSQTIYFLGL TALLLRYAQR NCTHSFYLVN AMSRNLFRVP KY INGTKLK NTMRKLKRKQ APVKEQSEKK SKKSQSTTTP YSPYTTSTAL NVTTNATYSV TTTARRVSTS TIAYRPDSSF MKS IMTTQL RDLATWVYTT LRYRQNPFCE SSRNRTAVSE FMKNTHVLIR NETPYTIYGT LDMSSLYYNE TMFVENKTAS ETTP TSPST GFQRTFIDPL WDYLDSLLFL DEIRNFSLQS PTYGNLTPPE HRRAVNLSTL NSLWWWLQ |
-分子 #4: Platelet-derived growth factor receptor alpha
分子 | 名称: Platelet-derived growth factor receptor alpha / タイプ: protein_or_peptide / ID: 4 / コピー数: 1 / 光学異性体: LEVO / EC番号: receptor protein-tyrosine kinase |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 59.370016 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MGTSHPAFLV LGCLLTGLSL ILCQLSLPSI LPNENEKVVQ LNSSFSLRCF GESEVSWQYP MSEEESSDVE IRNEENNSGL FVTVLEVSS ASAAHTGLYT CYYNHTQTEE NELEGRHIYI YVPDPDVAFV PLGMTDYLVI VEDDDSAIIP CRTTDPETPV T LHNSEGVV ...文字列: MGTSHPAFLV LGCLLTGLSL ILCQLSLPSI LPNENEKVVQ LNSSFSLRCF GESEVSWQYP MSEEESSDVE IRNEENNSGL FVTVLEVSS ASAAHTGLYT CYYNHTQTEE NELEGRHIYI YVPDPDVAFV PLGMTDYLVI VEDDDSAIIP CRTTDPETPV T LHNSEGVV PASYDSRQGF NGTFTVGPYI CEATVKGKKF QTIPFNVYAL KATSELDLEM EALKTVYKSG ETIVVTCAVF NN EVVDLQW TYPGEVKGKG ITMLEEIKVP SIKLVYTLTV PEATVKDSGD YECAARQATR EVKEMKKVTI SVHEKGFIEI KPT FSQLEA VNLHEVKHFV VEVRAYPPPR ISWLKNNLTL IENLTEITTD VEKIQEIRYR SKLKLIRAKE EDSGHYTIVA QNED AVKSY TFELLTQVPS SILDLVDDHH GSTGGQTVRC TAEGTPLPDI EWMICKDIKK CNNETSWTIL ANNVSNIITE IHPRD RSTV EGRVTFAKVE ETIAVRCLAK NLLGAENREL KLVAPTLRSE ENLYFQ |
-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
濃度 | 1.6 mg/mL |
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緩衝液 | pH: 7.5 / 詳細: 300mM NaCl and 20mM HEPES7.5 |
グリッド | モデル: Quantifoil R2/1 / 材質: GOLD / メッシュ: 200 / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 96 % / チャンバー内温度: 293 K / 装置: LEICA EM GP |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均電子線量: 75.0 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 / Cs: 2.7 mm / 最大 デフォーカス(公称値): 2.4 µm / 最小 デフォーカス(公称値): 0.8 µm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |