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基本情報
登録情報 | データベース: PDB / ID: 1hzh | |||||||||
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タイトル | CRYSTAL STRUCTURE OF THE INTACT HUMAN IGG B12 WITH BROAD AND POTENT ACTIVITY AGAINST PRIMARY HIV-1 ISOLATES: A TEMPLATE FOR HIV VACCINE DESIGN | |||||||||
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![]() | IMMUNE SYSTEM / immunoglobulin / antibody / b12 | |||||||||
機能・相同性 | ![]() IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / immunoglobulin complex / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / FCERI mediated NF-kB activation / Regulation of actin dynamics for phagocytic cup formation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane 類似検索 - 分子機能 | |||||||||
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手法 | ![]() ![]() ![]() | |||||||||
![]() | Saphire, E.O. / Burton, D.R. / Wilson, I.A. | |||||||||
![]() | ![]() タイトル: Crystal structure of a neutralizing human IGG against HIV-1: a template for vaccine design. 著者: Saphire, E.O. / Parren, P.W. / Pantophlet, R. / Zwick, M.B. / Morris, G.M. / Rudd, P.M. / Dwek, R.A. / Stanfield, R.L. / Burton, D.R. / Wilson, I.A. | |||||||||
履歴 |
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Remark 999 | Sequence The Genbank database sequence (AAA52919) is the correct match for the variable portion of ...Sequence The Genbank database sequence (AAA52919) is the correct match for the variable portion of the heavy chain except that the N-terminus has been changed from LEQSGAE to QVQLVQSGAE in the process of cloning from the recombinant Fab fragment to the IgG. The constant domains of the heavy chains H and K have the same sequence as all human IgG1 antibodies. The variable region of the light chain matches the Genbank database sequence (AAA52920) except that the N-terminus was changed in cloning to the IgG from ELTQAPG to EIVLTQSPG; the constant domains of the light chains L and M have the same sequence as all human kappa light chains. The authors maintain that the sequence of L and M, residue ALA 34 (residue number 35 in seqres) should be an ALA and not ARG (residue 33 -in the sequence database). |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 268.8 KB | 表示 | ![]() |
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-検証レポート
文書・要旨 | ![]() | 675.6 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 735.8 KB | 表示 | |
XML形式データ | ![]() | 60.8 KB | 表示 | |
CIF形式データ | ![]() | 79.1 KB | 表示 | |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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要素
#1: 抗体 | 分子量: 50473.652 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: P0DOX5, UniProt: P01857*PLUS #2: 抗体 | 分子量: 23707.354 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q8TCD0, UniProt: P01834*PLUS #3: 多糖 | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #4: 多糖 | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | #5: 水 | ChemComp-HOH / | Has protein modification | Y | |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 4.11 Å3/Da / 溶媒含有率: 69.8 % | ||||||||||||||||||||||||||||||
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結晶化 | 温度: 295.5 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5 詳細: NH4SO4, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K | ||||||||||||||||||||||||||||||
結晶化 | *PLUS pH: 7.2 / 詳細: Saphire, E.O., (2001) Acta Crystallogr., D57, 168. | ||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 96 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 1999年1月18日 / 詳細: 58 cm long, Pt-coated, fused silica, vertical focus |
放射 | モノクロメーター: Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus 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: 1.08 Å / 相対比: 1 |
反射 | 解像度: 2.7→29.65 Å / Num. obs: 187712 / % possible obs: 94.4 % / Observed criterion σ(I): -2 / 冗長度: 2.9 % / Biso Wilson estimate: 65.9 Å2 / Rsym value: 0.072 / Net I/σ(I): 17.6 |
反射 シェル | 解像度: 2.7→2.75 Å / 冗長度: 2.7 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3113 / Rsym value: 0.626 / % possible all: 95.5 |
反射 | *PLUS Num. obs: 63686 / Num. measured all: 187712 / Rmerge(I) obs: 0.072 |
反射 シェル | *PLUS % possible obs: 95.5 % / Num. unique obs: 3113 / Num. measured obs: 8424 / Rmerge(I) obs: 0.626 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: PDB ENTRY 1CBV human Fc coordinates (unpublished) 解像度: 2.7→29.65 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 433076.48 / Data cutoff high rms absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 49.44 Å2 / ksol: 0.301 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 90.1 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.7→29.65 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.7→2.87 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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ソフトウェア | *PLUS 名称: CNS / バージョン: 0.9 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.225 / Rfactor Rfree: 0.272 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 90.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.381 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.352 |