+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-31422 | |||||||||
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タイトル | Cryo-EM structure of the chemokine receptor CCR5 in complex with MIP-1a and Gi | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 chemokine (C-C motif) ligand 5 binding / granulocyte chemotaxis / lymphocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / regulation of behavior / signaling / chemokine receptor activity ...chemokine (C-C motif) ligand 5 binding / granulocyte chemotaxis / lymphocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / regulation of behavior / signaling / chemokine receptor activity / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation / regulation of sensory perception of pain / negative regulation of bone mineralization / CCR chemokine receptor binding / positive regulation of microglial cell activation / C-C chemokine receptor activity / cell activation / C-C chemokine binding / phosphatidylinositol phospholipase C activity / T cell chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dendritic cell chemotaxis / phospholipase activator activity / macrophage chemotaxis / positive regulation of calcium ion import / chemoattractant activity / monocyte chemotaxis / negative regulation of osteoclast differentiation / exocytosis / Interleukin-10 signaling / cellular response to interleukin-1 / negative regulation by host of viral transcription / Binding and entry of HIV virion / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / cellular defense response / regulation of cAMP-mediated signaling / coreceptor activity / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cytoskeleton organization / cellular response to forskolin / neutrophil chemotaxis / positive regulation of calcium-mediated signaling / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / cell chemotaxis / positive regulation of interleukin-1 beta production / Regulation of insulin secretion / G protein-coupled receptor binding / calcium-mediated signaling / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Glucagon signaling in metabolic regulation / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / cellular response to type II interferon / G beta:gamma signalling through CDC42 / response to peptide hormone / Vasopressin regulates renal water homeostasis via Aquaporins / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / G alpha (z) signalling events / Adrenaline,noradrenaline inhibits insulin secretion / response to toxic substance / intracellular calcium ion homeostasis / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / positive regulation of inflammatory response / osteoblast differentiation / cellular response to catecholamine stimulus / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / GPER1 signaling / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of tumor necrosis factor production / chemotaxis 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: 2.9 Å | |||||||||
データ登録者 | Zhang H / Chen K / Tan Q / Han S / Zhu Y / Zhao Q / Wu B | |||||||||
資金援助 | 中国, 2件
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引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: Structural basis for chemokine recognition and receptor activation of chemokine receptor CCR5. 著者: Hui Zhang / Kun Chen / Qiuxiang Tan / Qiang Shao / Shuo Han / Chenhui Zhang / Cuiying Yi / Xiaojing Chu / Ya Zhu / Yechun Xu / Qiang Zhao / Beili Wu / 要旨: The chemokine receptor CCR5 plays a vital role in immune surveillance and inflammation. However, molecular details that govern its endogenous chemokine recognition and receptor activation remain ...The chemokine receptor CCR5 plays a vital role in immune surveillance and inflammation. However, molecular details that govern its endogenous chemokine recognition and receptor activation remain elusive. Here we report three cryo-electron microscopy structures of G protein-coupled CCR5 in a ligand-free state and in complex with the chemokine MIP-1α or RANTES, as well as the crystal structure of MIP-1α-bound CCR5. These structures reveal distinct binding modes of the two chemokines and a specific accommodate pattern of the chemokine for the distal N terminus of CCR5. Together with functional data, the structures demonstrate that chemokine-induced rearrangement of toggle switch and plasticity of the receptor extracellular region are critical for receptor activation, while a conserved tryptophan residue in helix II acts as a trigger of receptor constitutive activation. | |||||||||
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_31422.map.gz | 59.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-31422-v30.xml emd-31422.xml | 13.7 KB 13.7 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_31422.png | 26 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-31422 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31422 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_31422_validation.pdf.gz | 471.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_31422_full_validation.pdf.gz | 471.3 KB | 表示 | |
XML形式データ | emd_31422_validation.xml.gz | 6 KB | 表示 | |
CIF形式データ | emd_31422_validation.cif.gz | 6.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31422 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31422 | 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_31422.map.gz / 形式: CCP4 / 大きさ: 64 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: 1.045 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
-試料の構成要素
-全体 : Chemokine receptor CCR5 in complex with MIP-1a and Gi
全体 | 名称: Chemokine receptor CCR5 in complex with MIP-1a and Gi |
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要素 |
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-超分子 #1: Chemokine receptor CCR5 in complex with MIP-1a and Gi
超分子 | 名称: Chemokine receptor CCR5 in complex with MIP-1a and Gi 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: Spodoptera frugiperda (ツマジロクサヨトウ) |
-分子 #1: C-C motif chemokine 3,C-C chemokine receptor type 5
分子 | 名称: C-C motif chemokine 3,C-C chemokine receptor type 5 / タイプ: protein_or_peptide / ID: 1 / 詳細: Fusion protein of MIP-1a and CCR5 / 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: 51.241047 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: SLAADTPTAC CFSYCSRQIP QNFIADYFET SSQCSKPGVI FLTKRSRQVC ADPSEEWVQK YVSDLELSAG SGSGSGSGSG SGSGSGSGS GSGSDYQVSS PIYDINYYCS EPCQKINVKQ IAARLLPPLY SLVFIFGFVG NMLVILILIN CKRLKSMTDI Y LLNLAISD ...文字列: SLAADTPTAC CFSYCSRQIP QNFIADYFET SSQCSKPGVI FLTKRSRQVC ADPSEEWVQK YVSDLELSAG SGSGSGSGSG SGSGSGSGS GSGSDYQVSS PIYDINYYCS EPCQKINVKQ IAARLLPPLY SLVFIFGFVG NMLVILILIN CKRLKSMTDI Y LLNLAISD LFFLLTVPFW AHYAAAQWDF GNTMCQLLTG LYFIGFFSGI FFIILLTIDR YLAVVHAVFA LKARTVTFGV VT SVITWVV AVFASLPNII FTRSQKEGLH YTCSSHFPYS QYQFWKNFQT LKIVILGLVL PLLVMVICYS GILKTLLRCR NEK KRHRAV RLIFTIMIVY FLFWAPYNIV LLLNTFQEFF GLNNCSSSNR LDQAMQVTET LGMTHCCINP IIYAFVGEKF RNYL LVFFQ KHIAKRLEVL FQGPGSWSHP QFEKGSGAGA SAGSWSHPQF EKGSDYKDDD DK |
-分子 #2: Guanine nucleotide-binding protein G(i) subunit alpha-1
分子 | 名称: Guanine nucleotide-binding protein G(i) subunit alpha-1 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: 40.447141 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKCTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...文字列: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKCTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVTAQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHASM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCS TDTKNVQFVF DAVTDVIIKN NLKDCGLF |
-分子 #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
分子 | 名称: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 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: Homo sapiens (ヒト) |
分子量 | 理論値: 37.41693 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...文字列: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN |
-分子 #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
分子 | 名称: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 タイプ: protein_or_peptide / ID: 4 / 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: 7.861143 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L |
-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: 7.5 |
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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 BIOQUANTUM (6k x 4k) 平均電子線量: 2.1875 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: SPOT SCAN / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 7095732 |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |