+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 1ddh | ||||||
---|---|---|---|---|---|---|---|
タイトル | MHC CLASS I H-2DD HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND AN IMMUNODOMINANT PEPTIDE P18-I10 FROM THE HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE GLYCOPROTEIN 120 | ||||||
![]() |
| ||||||
![]() | COMPLEX (HISTOCOMPATIBILITY/ANTIGEN) / COMPLEX (HISTOCOMPATIBILITY-ANTIGEN) / HISTOCOMPATIBILITY ANTIGEN / CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX / MHC I / COMPLEX (HISTOCOMPATIBILITY-ANTIGEN) complex | ||||||
機能・相同性 | ![]() Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / Neutrophil degranulation / host cell endosome membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / viral protein processing / immune response / fusion of virus membrane with host plasma membrane / lysosomal membrane / external side of plasma membrane / signaling receptor binding / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Li, H. / Margulies, D.H. / Mariuzza, R.A. | ||||||
![]() | ![]() タイトル: Three-dimensional structure of H-2Dd complexed with an immunodominant peptide from human immunodeficiency virus envelope glycoprotein 120. 著者: Li, H. / Natarajan, K. / Malchiodi, E.L. / Margulies, D.H. / Mariuzza, R.A. #1: ![]() タイトル: H-2Dd Exploits a Four Residue Peptide Binding Motif 著者: Corr, M. / Boyd, L.F. / Padlan, E.A. / Margulies, D.H. | ||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 82.4 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 65.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 430.5 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 450.4 KB | 表示 | |
XML形式データ | ![]() | 17.8 KB | 表示 | |
CIF形式データ | ![]() | 23.5 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 1vadS S: 精密化の開始モデル |
---|---|
類似構造データ |
-
リンク
-
集合体
登録構造単位 | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
単位格子 |
|
-
要素
#1: タンパク質 | 分子量: 31862.404 Da / 分子数: 1 / 断片: EXTRACELLULAR DOMAINS / 変異: G1M / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
---|---|
#2: タンパク質 | 分子量: 11678.388 Da / 分子数: 1 / 断片: EXTRACELLULAR DOMAIN / 変異: I1M / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
#3: タンパク質・ペプチド | 分子量: 1075.265 Da / 分子数: 1 / 断片: RESIDUES 308-322 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 属: Lentivirus / 参照: UniProt: P04582 |
#4: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 2.53 Å3/Da / 溶媒含有率: 58 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
結晶化 | pH: 6.5 / 詳細: pH 6.5 | |||||||||||||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法, ハンギングドロップ法詳細: drop solution was mixed with an equal volume of reservoir solution | |||||||||||||||||||||||||
溶液の組成 | *PLUS
|
-データ収集
回折 | 平均測定温度: 100 K |
---|---|
放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: MAR scanner 300 mm plate / 検出器: IMAGE PLATE / 日付: 1997年7月1日 |
放射 | 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 0.773 Å / 相対比: 1 |
反射 | 最高解像度: 3.1 Å / Num. obs: 33412 / % possible obs: 86.8 % / 冗長度: 3.6 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 12.7 |
反射 シェル | 解像度: 3.1→3.2 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.389 / % possible all: 75 |
反射 | *PLUS Num. obs: 7809 / % possible obs: 88 % / Num. measured all: 27938 / Rmerge(I) obs: 0.071 |
反射 シェル | *PLUS 最高解像度: 3.2 Å / 最低解像度: 3.3 Å / % possible obs: 81.4 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3 |
-
解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: ![]() 開始モデル: PDB ENTRY 1VAD 解像度: 3.1→8 Å / Data cutoff low absF: 0 / 交差検証法: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 3.1→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 3.1→3.2 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ソフトウェア | *PLUS 名称: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 3.2 Å / Num. reflection Rfree: 580 / Rfactor obs: 0.225 / Rfactor Rfree: 0.33 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | *PLUS 最高解像度: 3.2 Å / 最低解像度: 3.3 Å / Rfactor obs: 0.309 |