+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1nys | ||||||
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タイトル | Crystal Structure of Activin A Bound to the ECD of ActRIIB P41 | ||||||
要素 |
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キーワード | MEMBRANE PROTEIN/HORMONE/GROWTH FACTOR / ACTIVIN / TYPE II / TGF BETA / ACTRIIB / EXTRACELLULAR DOMAIN / MEMBRANE PROTEIN-HORMONE-GROWTH FACTOR COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 Signaling by BMP / inhibin-betaglycan-ActRII complex / activin A complex / inhibin A complex / cardiac fibroblast cell development / : / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / inhibin binding / positive regulation of ovulation ...Signaling by BMP / inhibin-betaglycan-ActRII complex / activin A complex / inhibin A complex / cardiac fibroblast cell development / : / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / inhibin binding / positive regulation of ovulation / GABAergic neuron differentiation / activin receptor activity, type II / Antagonism of Activin by Follistatin / negative regulation of follicle-stimulating hormone secretion / progesterone secretion / penile erection / lymphatic endothelial cell differentiation / type II activin receptor binding / striatal medium spiny neuron differentiation / positive regulation of activin receptor signaling pathway / Glycoprotein hormones / activin receptor activity / negative regulation of macrophage differentiation / venous blood vessel development / cellular response to oxygen-glucose deprivation / positive regulation of follicle-stimulating hormone secretion / Signaling by Activin / : / Sertoli cell proliferation / hemoglobin biosynthetic process / lymphangiogenesis / regulation of nitric-oxide synthase activity / sperm ejaculation / retina vasculature development in camera-type eye / BMP receptor activity / embryonic skeletal system development / sexual reproduction / embryonic foregut morphogenesis / activin receptor complex / cellular response to follicle-stimulating hormone stimulus / cellular response to cholesterol / artery development / pattern specification process / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / activin binding / Signaling by BMP / cellular response to BMP stimulus / activin receptor signaling pathway / negative regulation of phosphorylation / SMAD protein signal transduction / Signaling by Activin / kinase activator activity / mesodermal cell differentiation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / gastrulation with mouth forming second / cellular response to angiotensin / pancreas development / determination of left/right symmetry / negative regulation of cold-induced thermogenesis / insulin secretion / skeletal system morphogenesis / odontogenesis / positive regulation of transcription by RNA polymerase III / anterior/posterior pattern specification / organ growth / adrenal gland development / negative regulation of G1/S transition of mitotic cell cycle / response to aldosterone / roof of mouth development / eyelid development in camera-type eye / endodermal cell differentiation / growth factor binding / odontogenesis of dentin-containing tooth / mesoderm development / peptide hormone binding / positive regulation of SMAD protein signal transduction / negative regulation of type II interferon production / hair follicle development / positive regulation of collagen biosynthetic process / regulation of signal transduction / blood vessel remodeling / BMP signaling pathway / positive regulation of osteoblast differentiation / positive regulation of bone mineralization / hematopoietic progenitor cell differentiation / coreceptor activity / response to glucose / extrinsic apoptotic signaling pathway / ovarian follicle development / positive regulation of protein metabolic process / protein serine/threonine/tyrosine kinase activity / : / erythrocyte differentiation / positive regulation of erythrocyte differentiation / post-embryonic development / response to activity / kidney development / skeletal system development / cytokine activity 類似検索 - 分子機能 | ||||||
生物種 | Rattus norvegicus (ドブネズミ) Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 3.05 Å | ||||||
データ登録者 | Thompson, T.B. / Woodruff, T.K. / Jardetzky, T.S. | ||||||
引用 | ジャーナル: EMBO J. / 年: 2003 タイトル: Structures of an ActRIIB:activin A complex reveal a novel binding mode for TGF-beta ligand:receptor interactions 著者: Thompson, T.B. / Woodruff, T.K. / Jardetzky, T.S. | ||||||
履歴 |
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Remark 999 | SEQUENCE According to the depositor, Pro64 is a DNA sequence error in the database (PIR JQ1484). ...SEQUENCE According to the depositor, Pro64 is a DNA sequence error in the database (PIR JQ1484). The correct residue is Arg64. This has been confirmed by sequence alignment of orthologous proteins. |
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1nys.cif.gz | 81.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1nys.ent.gz | 60.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1nys.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ny/1nys ftp://data.pdbj.org/pub/pdb/validation_reports/ny/1nys | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 12341.596 Da / 分子数: 2 / 断片: N-terminal Extracellular Domain (residues 19-119) / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: actrIIb / プラスミド: pvl1392 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 株 (発現宿主): SF+ / 参照: UniProt: P38444, UniProt: P38445*PLUS #2: タンパク質 | 分子量: 12991.865 Da / 分子数: 2 / 断片: Mature Domain (residues 311-426) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: INHBA 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 株 (発現宿主): BA83.6-02 / 参照: UniProt: P08476 |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 3.45 Å3/Da / 溶媒含有率: 64.06 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 詳細: PEG 4000, sodium chloride, hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 113 K |
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放射光源 | 由来: シンクロトロン / サイト: APS / ビームライン: 5ID-B / 波長: 1 Å |
検出器 | タイプ: MARRESEARCH / 検出器: CCD / 日付: 2002年5月11日 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 1 Å / 相対比: 1 |
反射 | 解像度: 3.05→25 Å / Num. obs: 9789 / % possible obs: 93.5 % / 冗長度: 4.5 % / Biso Wilson estimate: 77 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.14 |
反射 シェル | 解像度: 3.05→3.1 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.9 |
反射 | *PLUS Num. measured all: 44194 |
反射 シェル | *PLUS % possible obs: 87 % |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 1BTE 解像度: 3.05→24.74 Å / Rfactor Rfree error: 0.014 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 30.6845 Å2 / ksol: 0.270069 e/Å3 | |||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 77 Å2
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Refine analyze | Luzzati coordinate error free: 0.52 Å / Luzzati sigma a free: 0.72 Å | |||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 3.05→24.74 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 3.05→3.24 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 6
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Xplor file |
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精密化 | *PLUS 最低解像度: 25 Å / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.251 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||
原子変位パラメータ | *PLUS | |||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS 最低解像度: 3.1 Å |