+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1qgc | ||||||
---|---|---|---|---|---|---|---|
タイトル | STRUCTURE OF THE COMPLEX OF A FAB FRAGMENT OF A NEUTRALIZING ANTIBODY WITH FOOT AND MOUTH DISEASE VIRUS | ||||||
要素 |
| ||||||
キーワード | Virus/Immune system / VIRUS-ANTIBODY COMPLEX / Icosahedral virus / Virus-Immune system COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 L-peptidase / symbiont-mediated perturbation of host chromatin organization / protein complex oligomerization / B cell differentiation / ribonucleoside triphosphate phosphatase activity / picornain 3C / monoatomic ion channel activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity ...L-peptidase / symbiont-mediated perturbation of host chromatin organization / protein complex oligomerization / B cell differentiation / ribonucleoside triphosphate phosphatase activity / picornain 3C / monoatomic ion channel activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / nucleoside-triphosphate phosphatase / monoatomic ion transmembrane transport / regulation of translation / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / viral protein processing / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / extracellular region / ATP binding / membrane / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | Foot-and-mouth disease virus - type C (ウイルス) Mus musculus (ハツカネズミ) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 30 Å | ||||||
データ登録者 | Fita, I. | ||||||
引用 | ジャーナル: EMBO J / 年: 1997 タイトル: Structure of the complex of an Fab fragment of a neutralizing antibody with foot-and-mouth disease virus: positioning of a highly mobile antigenic loop. 著者: E A Hewat / N Verdaguer / I Fita / W Blakemore / S Brookes / A King / J Newman / E Domingo / M G Mateu / D I Stuart / 要旨: Data from cryo-electron microscopy and X-ray crystallography have been combined to study the interactions of foot-and-mouth disease virus serotype C (FMDV-C) with a strongly neutralizing monoclonal ...Data from cryo-electron microscopy and X-ray crystallography have been combined to study the interactions of foot-and-mouth disease virus serotype C (FMDV-C) with a strongly neutralizing monoclonal antibody (mAb) SD6. The mAb SD6 binds to the long flexible GH-loop of viral protein 1 (VP1) which also binds to an integrin receptor. The structure of the virus-Fab complex was determined to 30 A resolution using cryo-electron microscopy and image analysis. The known structure of FMDV-C, and of the SD6 Fab co-crystallized with a synthetic peptide corresponding to the GH-loop of VP1, were fitted to the cryo-electron microscope density map. The SD6 Fab is seen to project almost radially from the viral surface in an orientation which is only compatible with monovalent binding of the mAb. Even taking into account the mAb hinge and elbow flexibility, it is not possible to model bivalent binding without severely distorting the Fabs. The bound GH-loop is essentially in what has previously been termed the 'up' position in the best fit Fab orientation. The SD6 Fab interacts almost exclusively with the GH-loop of VP1, making very few other contacts with the viral capsid. The position and orientation of the SD6 Fab bound to FMDV-C is in accord with previous immunogenic data. | ||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1qgc.cif.gz | 214.4 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb1qgc.ent.gz | 164.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1qgc.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
文書・要旨 | 1qgc_validation.pdf.gz | 406.8 KB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 1qgc_full_validation.pdf.gz | 467.2 KB | 表示 | |
XML形式データ | 1qgc_validation.xml.gz | 29.5 KB | 表示 | |
CIF形式データ | 1qgc_validation.cif.gz | 43.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/qg/1qgc ftp://data.pdbj.org/pub/pdb/validation_reports/qg/1qgc | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
対称性 | 点対称性: (ヘルマン・モーガン記号: 532 / シェーンフリース記号: I (正20面体型対称)) |
-要素
-PROTEIN (VIRUS CAPSID PROTEIN ... , 3種, 3分子 123
#1: タンパク質 | 分子量: 22667.582 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Foot-and-mouth disease virus - type C (ウイルス) 属: Aphthovirus / 生物種: Foot-and-mouth disease virus / 株: SEROTYPE C / 参照: UniProt: Q9QCE2, UniProt: P03311*PLUS |
---|---|
#2: タンパク質 | 分子量: 24297.367 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Foot-and-mouth disease virus - type C (ウイルス) 属: Aphthovirus / 生物種: Foot-and-mouth disease virus / 株: SEROTYPE C / 参照: UniProt: Q9QCE2, UniProt: P03311*PLUS |
#3: タンパク質 | 分子量: 24020.875 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Foot-and-mouth disease virus - type C (ウイルス) 属: Aphthovirus / 生物種: Foot-and-mouth disease virus / 株: SEROTYPE C / 参照: UniProt: P15072, UniProt: P03311*PLUS |
-タンパク質・ペプチド , 1種, 1分子 5
#6: タンパク質・ペプチド | 分子量: 2463.722 Da / 分子数: 1 / Fragment: RESIDUES 133-156 / 由来タイプ: 天然 由来: (天然) Foot-and-mouth disease virus - type C (ウイルス) 属: Aphthovirus / 生物種: Foot-and-mouth disease virus / 株: SEROTYPE C / 参照: UniProt: P03311*PLUS |
---|
-抗体 , 2種, 2分子 4A
#4: 抗体 | 分子量: 24013.379 Da / 分子数: 1 / Fragment: FAB / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: P01837*PLUS |
---|---|
#5: 抗体 | 分子量: 23442.508 Da / 分子数: 1 / Fragment: FAB / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: FAB FRAGMENT OF A NEUTRALIZING ANTIBODY WITH FOOT AND MOUTH DISEASE VIRUS タイプ: COMPLEX | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | |||||||||||||||
試料支持 | Film material: HOLEY CARBON / グリッドのサイズ: 400 divisions/in. | |||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法 | |||||||||||||||
溶液の組成 | *PLUS
|
-電子顕微鏡撮影
顕微鏡 | モデル: JEOL 2000EXII |
---|---|
電子銃 | 加速電圧: 100 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 30000 X / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1800 nm |
撮影 | 電子線照射量: 20 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
-解析
EMソフトウェア |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
対称性 | 点対称性: I (正20面体型対称) | ||||||||||||||||
3次元再構成 | 対称性のタイプ: POINT | ||||||||||||||||
原子モデル構築 | 空間: REAL 詳細: DETAILS--THE ATOMIC MODEL WAS GENERATED USING THE 3D MAP DETERMINED BY CRYO-ELECTRON MICROSCOPY. X-RAY ATOMIC STRUCTURES WERE AVAILABLE FOR THE INTACT PARTICLE OF FMDV-C AND THE SD6 FAB CO- ...詳細: DETAILS--THE ATOMIC MODEL WAS GENERATED USING THE 3D MAP DETERMINED BY CRYO-ELECTRON MICROSCOPY. X-RAY ATOMIC STRUCTURES WERE AVAILABLE FOR THE INTACT PARTICLE OF FMDV-C AND THE SD6 FAB CO-CRYSTALLIZED WITH A SYNTHETIC PEPTIDE CORRESPONDING TO THE DOMINANT ANTIGENIC LOOP, THE GH LOOP, FROM THE VIRAL CAPSIDE PROTEIN VP1. THE ATOMIC MODEL WAS OBTAINED BY DOCKING THE TWO CRYSTALLOGRAPHIC STRUCTURES IN THE RECONSTRUCTED EM MAP. FITTING WAS DONE SIMULTANEOUSLY IN REAL AND RECIPROCAL SPACE. IN REAL SPACE THE CALCULATED ELECTRON DENSITY FOR THE STARTING MODELS WERE FITTED INTO THE CRYO-EM DENSITY BY A STEEPEST DESCENT PROCEDURE WHICH OPTIMIZED THE LINEAR CORRELATION COEFFICIENT BETWEEN THE TWO DISTRIBUTION (GAP- J.GRIMES,D.STUART, UNPUBLISHED) FOR THE RECIPROCAL SPACE FITTING THE STRUCTURE FACTORS CORRESPONDING TO THE CRYO-EM DENSITY OF THE COMPLEX WERE CALCULATED BY INVERSE FOURIER TRANSFORMATIONS AND THESE FACTORS AND PHASES WERE USED TO REFINE THE X-RAY STRUCTURES, BY RIGID BODY MINIMIZATION, USING X-PLOR (BRUNGER, ET.AL., 1993, YALE UNIVERSITY) | ||||||||||||||||
原子モデル構築 | PDB-ID: 1FMD Accession code: 1FMD / Source name: PDB / タイプ: experimental model | ||||||||||||||||
精密化 | 最高解像度: 30 Å | ||||||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 30 Å
|