+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-18742 | |||||||||||||||
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タイトル | Structure of interleukin 6. | |||||||||||||||
マップデータ | Sharpened map. | |||||||||||||||
試料 |
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キーワード | interleukin / gp130 / IMMUNE SYSTEM | |||||||||||||||
機能・相同性 | 機能・相同性情報 oncostatin-M receptor activity / ciliary neurotrophic factor binding / positive regulation of interleukin-21 production / regulation of astrocyte activation / IL-6-type cytokine receptor ligand interactions / glucagon secretion / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling ...oncostatin-M receptor activity / ciliary neurotrophic factor binding / positive regulation of interleukin-21 production / regulation of astrocyte activation / IL-6-type cytokine receptor ligand interactions / glucagon secretion / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / triglyceride mobilization / interleukin-6 receptor activity / interleukin-6 binding / regulation of glucagon secretion / Interleukin-6 signaling / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / Interleukin-35 Signalling / regulation of vascular endothelial growth factor production / oncostatin-M receptor complex / negative regulation of primary miRNA processing / ciliary neurotrophic factor receptor binding / interleukin-11 receptor activity / interleukin-11 binding / T follicular helper cell differentiation / ciliary neurotrophic factor-mediated signaling pathway / germinal center B cell differentiation / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / interleukin-6 receptor complex / positive regulation of extracellular matrix disassembly / positive regulation of receptor signaling pathway via STAT / positive regulation of apoptotic DNA fragmentation / response to peptidoglycan / positive regulation of type B pancreatic cell apoptotic process / regulation of microglial cell activation / hepatocyte proliferation / neutrophil apoptotic process / regulation of Notch signaling pathway / interleukin-6 receptor binding / negative regulation of collagen biosynthetic process / : / interleukin-11-mediated signaling pathway / inflammatory response to wounding / T-helper 17 cell lineage commitment / positive regulation of T-helper 2 cell cytokine production / positive regulation of B cell activation / endocrine pancreas development / positive regulation of glomerular mesangial cell proliferation / negative regulation of interleukin-8 production / positive regulation of acute inflammatory response / regulation of neuroinflammatory response / vascular endothelial growth factor production / positive regulation of astrocyte differentiation / negative regulation of chemokine production / positive regulation of neuroinflammatory response / positive regulation of leukocyte chemotaxis / intestinal epithelial cell development / positive regulation of platelet aggregation / positive regulation of cytokine production involved in inflammatory response / neutrophil mediated immunity / cytokine receptor activity / negative regulation of bone resorption / positive regulation of leukocyte adhesion to vascular endothelial cell / CD163 mediating an anti-inflammatory response / positive regulation of immunoglobulin production / glycogen metabolic process / interleukin-6-mediated signaling pathway / maintenance of blood-brain barrier / Interleukin-6 signaling / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / negative regulation of cytosolic calcium ion concentration / neuronal cell body membrane / protein tyrosine kinase activator activity / positive regulation of smooth muscle cell migration / MAPK3 (ERK1) activation / monocyte chemotaxis / positive regulation of interleukin-17 production / Interleukin-10 signaling / cytokine binding / MAPK1 (ERK2) activation / regulation of insulin secretion / positive regulation of interleukin-10 production / humoral immune response / negative regulation of lipid storage / Transcriptional Regulation by VENTX / positive regulation of vascular endothelial growth factor production / regulation of angiogenesis / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of epithelial to mesenchymal transition / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / positive regulation of T cell proliferation / response to glucocorticoid / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of glial cell proliferation / positive regulation of interleukin-1 beta production / response to activity 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: 3.1 Å | |||||||||||||||
データ登録者 | Gardner S / Bubeck D / Jin Y | |||||||||||||||
資金援助 | 英国, European Union, 4件
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引用 | ジャーナル: Acta Crystallogr D Struct Biol / 年: 2019 タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. 著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / ...著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / 要旨: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | |||||||||||||||
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_18742.map.gz | 323.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-18742-v30.xml emd-18742.xml | 23.9 KB 23.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_18742_fsc.xml | 14.8 KB | 表示 | FSCデータファイル |
画像 | emd_18742.png | 113.9 KB | ||
Filedesc metadata | emd-18742.cif.gz | 7.2 KB | ||
その他 | emd_18742_additional_1.map.gz emd_18742_additional_2.map.gz emd_18742_half_map_1.map.gz emd_18742_half_map_2.map.gz | 167 MB 3.4 MB 318 MB 318 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-18742 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18742 | HTTPS FTP |
-関連構造データ
関連構造データ | 8qy5MC 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_18742.map.gz / 形式: CCP4 / 大きさ: 343 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Sharpened map. | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.07 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: Unsharpened map.
ファイル | emd_18742_additional_1.map | ||||||||||||
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注釈 | Unsharpened map. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Locally filtered map.
ファイル | emd_18742_additional_2.map | ||||||||||||
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注釈 | Locally filtered map. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 2.
ファイル | emd_18742_half_map_1.map | ||||||||||||
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注釈 | Half map 2. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 1.
ファイル | emd_18742_half_map_2.map | ||||||||||||
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注釈 | Half map 1. | ||||||||||||
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 : IL-6 signalling complex
全体 | 名称: IL-6 signalling complex |
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要素 |
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-超分子 #1: IL-6 signalling complex
超分子 | 名称: IL-6 signalling complex / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#3 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: Interleukin-6 receptor subunit beta
分子 | 名称: Interleukin-6 receptor subunit beta / タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 102.552867 KDa |
組換発現 | 生物種: Trichoplusia ni (イラクサキンウワバ) |
配列 | 文字列: MSAPRIWLAQ ALLFFLTTES IGQLLEPCGY IYPEFPVVQR GSNFTAICVL KEACLQHYYV NASYIVWKTN HAAVPREQVT VINRTTSSV TFTDVVLPSV QLTCNILSFG QIEQNVYGVT MLSGFPPDKP TNLTCIVNEG KNMLCQWDPG RETYLETNYT L KSEWATEK ...文字列: MSAPRIWLAQ ALLFFLTTES IGQLLEPCGY IYPEFPVVQR GSNFTAICVL KEACLQHYYV NASYIVWKTN HAAVPREQVT VINRTTSSV TFTDVVLPSV QLTCNILSFG QIEQNVYGVT MLSGFPPDKP TNLTCIVNEG KNMLCQWDPG RETYLETNYT L KSEWATEK FPDCQSKHGT SCMVSYMPTY YVNIEVWVEA ENALGKVSSE SINFDPVDKV KPTPPYNLSV TNSEELSSIL KL SWVSSGL GGLLDLKSDI QYRTKDASTW IQVPLEDTMS PRTSFTVQDL KPFTEYVFRI RSIKDSGKGY WSDWSEEASG TTY EDRPSR PPSFWYKTNP SHGQEYRSVR LIWKALPLSE ANGKILDYEV ILTQSKSVSQ TYTVTGTELT VNLTNDRYVA SLAA RNKVG KSAAAVLTIP SPHVTAAYSV VNLKAFPKDN LLWVEWTPPP KPVSKYILEW CVLSENAPCV EDWQQEDATV NRTHL RGRL LESKCYQITV TPVFATGPGG SESLKAYLKQ AAPARGPTVR TKKVGKNEAV LAWDQIPVDD QNGFIRNYSI SYRTSV GKE MVVHVDSSHT EYTLSSLSSD TLYMVRMAAY TDEGGKDGPE FTFTTPKFAQ GEIEAIVVPV CLAFLLTTLL GVLFCFN KR DLIKKHIWPN VPDPSKSHIA QWSPHTPPRH NFNSKDQMYS DGNFTDVSVV EIEANNKKPC PDDLKSVDLF KKEKVSTE G HSSGIGGSSC MSSSRPSISS NEENESAQST ASTVQYSTVV HSGYRHQVPS VQVFSRSEST QPLLDSEERP EDLQLVDSV DGGDEILPRQ PYFKQNCSQP EACPEISHFE RSNQVLSGNE EDFVRLKQQQ VSDHISQPYG SEQRRLFQEG STADALGTGA DGQMERFES VGMETTIDEE IPKSYLPQTV RQGGYMPQ UniProtKB: Interleukin-6 receptor subunit beta |
-分子 #2: Interleukin-6
分子 | 名称: Interleukin-6 / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 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: 23.743189 KDa |
組換発現 | 生物種: Trichoplusia ni (イラクサキンウワバ) |
配列 | 文字列: MNSFSTSAFG PVAFSLGLLL VLPAAFPAPV PPGEDSKDVA APHRQPLTSS ERIDKQIRYI LDGISALRKE TCNKSNMCES SKEALAENN LNLPKMAEKD GCFQSGFNEE TCLVKIITGL LEFEVYLEYL QNRFESSEEQ ARAVQMSTKV LIQFLQKKAK N LDAITTPD ...文字列: MNSFSTSAFG PVAFSLGLLL VLPAAFPAPV PPGEDSKDVA APHRQPLTSS ERIDKQIRYI LDGISALRKE TCNKSNMCES SKEALAENN LNLPKMAEKD GCFQSGFNEE TCLVKIITGL LEFEVYLEYL QNRFESSEEQ ARAVQMSTKV LIQFLQKKAK N LDAITTPD PTTNASLLTK LQAQNQWLQD MTTHLILRSF KEFLQSSLRA LRQM UniProtKB: Interleukin-6 |
-分子 #3: Interleukin-6 receptor subunit alpha
分子 | 名称: Interleukin-6 receptor subunit alpha / タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 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: 51.605348 KDa |
組換発現 | 生物種: Trichoplusia ni (イラクサキンウワバ) |
配列 | 文字列: MLAVGCALLA ALLAAPGAAL APRRCPAQEV ARGVLTSLPG DSVTLTCPGV EPEDNATVHW VLRKPAAGSH PSRWAGMGRR LLLRSVQLH DSGNYSCYRA GRPAGTVHLL VDVPPEEPQL SCFRKSPLSN VVCEWGPRST PSLTTKAVLL VRKFQNSPAE D FQEPCQYS ...文字列: MLAVGCALLA ALLAAPGAAL APRRCPAQEV ARGVLTSLPG DSVTLTCPGV EPEDNATVHW VLRKPAAGSH PSRWAGMGRR LLLRSVQLH DSGNYSCYRA GRPAGTVHLL VDVPPEEPQL SCFRKSPLSN VVCEWGPRST PSLTTKAVLL VRKFQNSPAE D FQEPCQYS QESQKFSCQL AVPEGDSSFY IVSMCVASSV GSKFSKTQTF QGCGILQPDP PANITVTAVA RNPRWLSVTW QD PHSWNSS FYRLRFELRY RAERSKTFTT WMVKDLQHHC VIHDAWSGLR HVVQLRAQEE FGQGEWSEWS PEAMGTPWTE SRS PPAENE VSTPMQALTT NKDDDNILFR DSANATSLPV QDSSSVPLPT FLVAGGSLAF GTLLCIAIVL RFKKTWKLRA LKEG KTSMH PPYSLGQLVP ERPRPTPVLV PLISPPVSPS SLGSDNTSSH NRPDARDPRS PYDISNTDYF FPR UniProtKB: Interleukin-6 receptor subunit alpha |
-分子 #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
分子 | 名称: 2-acetamido-2-deoxy-beta-D-glucopyranose / タイプ: ligand / ID: 5 / コピー数: 2 / 式: NAG |
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分子量 | 理論値: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-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: 7.2 |
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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 (6k 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 / 最大 デフォーカス(公称値): 2.25 µm / 最小 デフォーカス(公称値): 0.5 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |