+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3hqv | |||||||||
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タイトル | Low resolution, molecular envelope structure of type I collagen in situ determined by fiber diffraction. Single type I collagen molecule, rigid body refinement | |||||||||
要素 |
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キーワード | STRUCTURAL PROTEIN (タンパク質) / CONTRACTILE PROTEIN / NATIVE / IN SITU (In situ) / Molecular envelope / TRIPLE-helical / SUPERMOLECULAR / supramolecular / PACKING STRUCTURE / STRUCTURAL PROTEIN-CONTRACTILE PROTEIN COMPLEX (構造) / Collagen (コラーゲン) / Extracellular matrix (細胞外マトリックス) / Glycoprotein (糖タンパク質) / Hydroxylation (ヒドロキシル化) / Pyrrolidone carboxylic acid (ピログルタミン酸) / Secreted (分泌) | |||||||||
機能・相同性 | 機能・相同性情報 Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Crosslinking of collagen fibrils / Non-integrin membrane-ECM interactions / Platelet Adhesion to exposed collagen / Platelet Aggregation (Plug Formation) / Collagen chain trimerization / MET activates PTK2 signaling / response to norepinephrine / GP1b-IX-V activation signalling ...Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Crosslinking of collagen fibrils / Non-integrin membrane-ECM interactions / Platelet Adhesion to exposed collagen / Platelet Aggregation (Plug Formation) / Collagen chain trimerization / MET activates PTK2 signaling / response to norepinephrine / GP1b-IX-V activation signalling / GPVI-mediated activation cascade / Cell surface interactions at the vascular wall / Assembly of collagen fibrils and other multimeric structures / Integrin cell surface interactions / response to fluoride / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / ECM proteoglycans / cellular response to fluoride / collagen type I trimer / tooth mineralization / protein heterotrimerization / cellular response to vitamin E / bone trabecula formation / extracellular matrix assembly / Collagen degradation / collagen biosynthetic process / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / collagen metabolic process / intramembranous ossification / embryonic skeletal system development / cartilage development involved in endochondral bone morphogenesis / skin morphogenesis / collagen-activated tyrosine kinase receptor signaling pathway / endochondral ossification / collagen trimer / cellular response to fibroblast growth factor stimulus / cellular response to thyroid hormone stimulus / collagen fibril organization / face morphogenesis / negative regulation of cell-substrate adhesion / skeletal system morphogenesis / response to steroid hormone / skin development / extracellular matrix structural constituent / cellular response to organic substance / blood vessel development / bone mineralization / SMAD binding / Rho protein signal transduction / protein localization to nucleus / response to hyperoxia / positive regulation of epithelial to mesenchymal transition / response to mechanical stimulus / cellular response to retinoic acid / response to cAMP / cellular response to epidermal growth factor stimulus / cellular response to transforming growth factor beta stimulus / 細胞外マトリックス / 視覚 / extracellular matrix organization / 骨化 / response to nutrient levels / response to nutrient / transforming growth factor beta receptor signaling pathway / 分泌 / skeletal system development / cellular response to glucose stimulus / cellular response to amino acid stimulus / sensory perception of sound / response to insulin / response to hydrogen peroxide / response to organic cyclic compound / response to peptide hormone / osteoblast differentiation / 血圧 / cellular response to mechanical stimulus / positive regulation of canonical Wnt signaling pathway / protein-macromolecule adaptor activity / protein transport / response to estradiol / cellular response to tumor necrosis factor / collagen-containing extracellular matrix / protease binding / positive regulation of cell migration / response to xenobiotic stimulus / positive regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding / metal ion binding / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Rattus norvegicus (ドブネズミ) | |||||||||
手法 | 繊維回折 / シンクロトロン / 多重同系置換 / 解像度: 5.16 Å | |||||||||
データ登録者 | Orgel, J.P. | |||||||||
引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2006 タイトル: Microfibrillar Structure of Type I Collagen in Situ 著者: Orgel, J.P. / Irving, T.C. / Miller, A. / Wess, T.J. | |||||||||
履歴 |
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-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 | 3hqv.cif.gz | 120 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3hqv.ent.gz | 70.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3hqv.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/hq/3hqv ftp://data.pdbj.org/pub/pdb/validation_reports/hq/3hqv | 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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単位格子 |
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詳細 | BIOMOLECULE: THIS ENTRY CONTAINS ONE COLLAGEN TYPE I MOLECULE. FOR RELATION TO THE FIBRILLAR PACKING OF COLLAGEN MOLECULES/MICRO-FIBRIL, REFER TO CITATION. IN SUMMARY: EACH COLLAGEN MOLECULE IS STAGGERED BY AN INTEGER MULTIPLE OF THE C-CELL AXIS. THE STRUCTURE CAN BE EXTENDED IN THE AXIAL (~C-CELL AXIS) DIRECTION BY APPLYING THE FOLLOWING TRANSLATION: NX,0Y,NZ TO THE MOLECULE, WHERE N IS AN INTEGER. A VISUALIZATION OF FIVE SUCCESSIVE 'D'-REPEATS OF THE BIOMOLECULE / MICRO-FIBRIL CAN BE OBTAINED FROM THESE COORDINATES BY APPLYING THE FOLLOWING TRANSLATIONS TO NINE COORDINATE SETS: A) 0, 0, 0; B) -1, 0,-1; C) -2, 0,-2; D) -3, 0,-3; E) -4, 0,-4; B1) 1, 0, 1; C1) 2, 0, 2; D1) 3, 0, 3; E1) 4, 0, 4. |
-要素
#1: タンパク質 | 分子量: 96747.344 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Rattus norvegicus (ドブネズミ) / 組織: tail tendon / 参照: UniProt: P02454 #2: タンパク質 | | 分子量: 93481.273 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Rattus norvegicus (ドブネズミ) / 組織: tail tendon / 参照: UniProt: P02466 |
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-実験情報
-実験
実験 | 手法: 繊維回折 / 使用した結晶の数: 6 |
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-試料調製
結晶 | 解説: THE RESOLUTION LIMITS FOR THE DATA COLLECTION ARE 38.5 TO 11.1A LATERAL AND 112.6 TO 5.16A AXIAL, INTENSITY-INTEGRATION SOFTWARE : FIT2D/IN-HOUSE, DATA SCALING SOFTWARE : IN-HOUSE |
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-データ収集
回折 | 平均測定温度: 298 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: 18-ID / 波長: 1.03 |
検出器 | タイプ: FUJI / 検出器: IMAGE PLATE / 日付: 1998年11月15日 / 詳細: MIRRORS |
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: 1.03 Å / 相対比: 1 |
反射 | 解像度: 5.16→112.6 Å / Num. all: 436 / Num. obs: 424 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
反射 シェル | 解像度: 5.16→112.6 Å / % possible all: 97 |
-解析
ソフトウェア | 名称: CNS / 分類: 精密化 | ||||||||||||
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精密化 | 構造決定の手法: 多重同系置換 / 解像度: 5.16→112.62 Å / σ(F): 1 / 立体化学のターゲット値: Engh & Huber 詳細: 305 EQUATORIAL AND 109 MERIDIONAL REFLECTIONS WERE USED FOR REFINEMENT WITH CNS. INITIAL REFINEMENT OF WHOLE MOLECULAR PATHS WAS PERFORMED IN THE STEPWISE FASHION DESCRIBED IN THE CITED ...詳細: 305 EQUATORIAL AND 109 MERIDIONAL REFLECTIONS WERE USED FOR REFINEMENT WITH CNS. INITIAL REFINEMENT OF WHOLE MOLECULAR PATHS WAS PERFORMED IN THE STEPWISE FASHION DESCRIBED IN THE CITED PUBLICATION. MODEL STRUCTURE FACTORS WHERE INITIALLY GENERATED FROM THE WHOLE RESIDUE SCATTERING FACTORS OF HULMES ET AL 1977 WHICH WERE SUBSTITUTED FOR THE CALPHA POSITIONS AND THE SQUARE FC'S WERE CALCULATED FOR COMPARISON BETWEEN A SIMULATED DIFFRACTION PATTERN AND THE OBSERVED PATTERNS. STRUCTURE FACTORS FROM THE FINAL MODEL WERE GENERATED IN THE NORMAL MANNER FOR REFINEMENT OF THE TELOPEPTIDE CONFORMATIONS USING CNS (SEE ABOVE). TWO ROUNDS OF Q-FACTOR REFINEMENT FOLLOWED BY ONE ROUND OF CONSTRAINED THEN UNCONSTRAINED ANNEALING FOR THE WHOLE STRUCTURE. THE R- FACTOR WHEN MEASURED VIA SIMULATED/OBSERVED DIFFRACTION PATTERN COMPARISON WAS FOUND TO BE 16.7% AND 6.6% BY MEASURE OF THE INTERGRATED STRUCTURE FACTORS. REFLECTIONS MISSING FROM THE MERIDONAL(OOL) SERIES WERE EITHER TOO WEAK TO MEASURE AND/OR VAIRED SIGNIFICANTLY BETWEEN COLLECTED PATTERNS (SEVEN IN TOTAL). THE FIRST FIVE REFLECTIONS WHERE EXCLUDED DUE TO THEIR LOW RESOLUTION (677.9 TO ~120 ANGSTROMS). EXLUDED REFLECTIONS ARE NOT INCLUDED IN THE 414 TOTAL. THE COORDINATES CONTAIN CA ATOMS ONLY.
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精密化ステップ | サイクル: LAST / 解像度: 5.16→112.62 Å
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