+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1hqy | ||||||
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タイトル | Nucleotide-Dependent Conformational Changes in a Protease-Associated ATPase HslU | ||||||
要素 |
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キーワード | CHAPERONE / HSLVU / PEPTIDASE-ATPASE COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 HslU-HslV peptidase / protein denaturation / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidase activity / cellular response to heat ...HslU-HslV peptidase / protein denaturation / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidase activity / cellular response to heat / response to heat / protein domain specific binding / magnesium ion binding / ATP hydrolysis activity / proteolysis / ATP binding / identical protein binding / membrane / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Escherichia coli (大腸菌) | ||||||
手法 | X線回折 / 解像度: 2.8 Å | ||||||
データ登録者 | Wang, J. / Song, J.J. / Seong, I.S. / Franklin, M.C. / Kamtekar, S. / Eom, S.H. / Chung, C.H. | ||||||
引用 | ジャーナル: Structure / 年: 2001 タイトル: Nucleotide-dependent conformational changes in a protease-associated ATPase HsIU. 著者: Wang, J. / Song, J.J. / Seong, I.S. / Franklin, M.C. / Kamtekar, S. / Eom, S.H. / Chung, C.H. #1: ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2000 タイトル: Mutational Studies of Hslu and its Docking Mode With Hslv. 著者: Song, H.K. / Hartmann, C. / Ramachandran, R. / Bochtler, M. / Behrendt, R. / Moroder, L. / Huber, R. #2: ジャーナル: Nature / 年: 2000 タイトル: The Structures of Hslu and the ATP-Dependent Protease HslU-HslV. 著者: Bochtler, M. / Hartmann, C. / Song, H.K. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R. #3: ジャーナル: Cell(Cambridge,Mass.) / 年: 2000 タイトル: Crystal and Solution Structures of an HslUV Protease-chaperone Complex. 著者: Sousa, M.C. / Trame, C.B. / Tsuruta, S. / Wilbanks, S.M. / Reddy, V.S. / McKay, D.B. #4: ジャーナル: Structure / 年: 2001 タイトル: Crystal Structures of the Hslvu Peptidase-ATPase Complex Reveal an ATP-Dependent Proteolysis Mechanism 著者: Wang, J. / Song, J.J. / Franklin, M.C. / Kamtekar, S. / Im, Y.J. / Rho, S.H. / Seong, I.S. / Lee, C.S. / Chung, C.H. / Eom, S.H. #5: ジャーナル: Nature / 年: 2000 タイトル: ATP-dependent proteases: Docking of Components in a Bacterial Complex 著者: Ishikawa, T. / Maurizi, M.R. / Belnap, D. / Steven, A.C. #6: ジャーナル: J.STRUCT.BIOL. / 年: 2001 タイトル: A corrected quaternary arrangement of the peptidase hslv and atpase hslu in a cocrystal structure 著者: Wang, J. | ||||||
履歴 |
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Remark 600 | HETEROGEN ADP 450 IS ASSOCIATED WITH CHAIN E. ADP 1450 IS ASSOCIATED WITH CHAIN F. |
-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 | 1hqy.cif.gz | 301.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1hqy.ent.gz | 243.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1hqy.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/1hqy ftp://data.pdbj.org/pub/pdb/validation_reports/hq/1hqy | 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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2 |
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単位格子 |
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詳細 | Dodecameric HslV complexed with hexameric HslU |
-要素
#1: タンパク質 | 分子量: 18986.641 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 株: BL21(DE3) / 細胞内の位置: CYTOPLASM / プラスミド: PET12B / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: P31059, UniProt: P0A7B8*PLUS #2: タンパク質 | 分子量: 50495.531 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 株: BL21(DE3) / 細胞内の位置: CYTOPLASM / プラスミド: PET12B / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: P0A6H5 #3: 化合物 | |
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-実験情報
-実験
実験 | 手法: X線回折 |
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-試料調製
結晶 | マシュー密度: 3.34 Å3/Da / 溶媒含有率: 63.14 % |
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結晶化 | 手法: see 1e94 / 詳細: SEE 1E94 |
-データ収集
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 |
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放射波長 | 相対比: 1 |
反射 | Biso Wilson estimate: 66.1 Å2 |
-解析
ソフトウェア | 名称: CNS / バージョン: 1 / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||
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精密化 | 解像度: 2.8→29.62 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 683901.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 詳細: THIS ENTRY CONTAINS A PSEUDO-SOLUTION IN X-RAY STRUCTURES TO THE X-RAY DIFFRACTION DATA THAT WERE RETRIEVED FROM PDB DATABASE UNDER ACCESSION NUMBER 1E94. THIS AUTHOR BELIEVES THIS ENTRY, ...詳細: THIS ENTRY CONTAINS A PSEUDO-SOLUTION IN X-RAY STRUCTURES TO THE X-RAY DIFFRACTION DATA THAT WERE RETRIEVED FROM PDB DATABASE UNDER ACCESSION NUMBER 1E94. THIS AUTHOR BELIEVES THIS ENTRY, WHICH HAS BEEN REVISED FROM THE ENTRY 1E94, IS A PSEUDO-SOLUTION, BECAUSE THE SPACE GROUP WAS INCORRECT ASSIGNED AND X-RAY DIFFRACTION DATA WERE INCORRECTLY AVERAGED AND PROCESSED IN 1E94. THE ASSIGNMENT OF THE SCREW AXIS 6(3) IN THE P6(3)22 SPACE GROUP FOR THE HSLVU COMPLEX STRUCTURES DESCRIBED IN REFERENCES 1 AND 2 BELOW (CORRESPONDING PDB ACCESSION NUMBERS ARE 1DOO AND 1E94, RESPECTIVELY) REQUIRES THE PRESENCE OF SYSTEMATIC EXTINCTIONS ALONG (00L) WITH L=2N+1. THERE WERE NO SYSTEMATIC EXTINCTIONS AT ALL IN THE 1E94SF ENTRY. THERE WERE TWO REFLECTIONS WITH F/SIGMA(F) NEAR 20 AND NINE REFLECTIONS WITH F/SIMGA(F) OVER 10 ALONG (00L) WITH L=2N+1. SUCH A LARGE NUMBER OF SIGNIFICANT OBSERVATIONS CANNOT BE DUE TO TECHNICAL ERRORS IN MEASUREMENT OF X-RAY DIFFRACTION DATA. A STATISTICAL ANALYSIS OF THEM COMPARED WITH THE REST OF THE DATA CONFIRMS THAT THEY ARE NOT DUE TO TECHNICAL ERRORS. THEREFORE, THE SPACE GROUP MUST NOT BE P6(3)22. LARGE VALUES OF COMBINED R-MERGE VALUES FOR OBSERVED DATA 1DOO (14.1%) AND 1E94 (12.1%) ARE INDICATIVE OF INCORRECT ASSIGNEMENT OF POINT SYMMETRY GROUP TO BE 622. THE ESTIMATED MEASUREMENT PRECISION IN INTENSITY SHOULD BE ABOUT 1% ON THE BASIS OF THE AVERAGE F/SIGMA(F) OF 44.7 IN 1E94 OBSERVED DATA. THEREFORE, ONE SETS OF DYADS IN THE POINT SYMMETRY P622 WERE TWINNING OPERATIONS. THERE WERE LARGE DISCREPANCIES IN WILSON RATIO (/^2) BETWEEN THE OBSERVED DATA AND CALCULATED DATA FROM THE COORDINATE 1E94 IN THE FOLLOWING ZONES: L=2N, L=2N+1, H+K=3N/L=2N; H+K != 3N/L=2N, AND ALL HKL. SOME WERE LARGE THAN 70% AND SOME WERE AS SMALL AS 5%. THIS SUGGESTS THAT X-RAY DATA WERE PROCESSED FROM TWINNED CRYSTALS. THERE WERE ALSO LARGE DIFFERENCES IN THE FIRST AND SECOND MOMENTS OF THE DIFFERENCES (FOBS-FCALC). THIS IS ANOTHER STATISTICAL INDICATOR FOR THE TWINNING PROBLEM. BECAUSE OF THE SEVERE ERRORS IN SPACE GROUP ASSIGNMENT AND DATA PROCESSING, ANY STRUCTURAL SOLUTIONS ARE PSEUDO-SOLUTIONS, WHICH FIT ONLY A PORTION OF THE ORIGINAL OBSERVATIONS. DESPITE OF THESE SEVERE ERRORS, USING THE OBSERVED 1E94 DATA, THIS AUTHOR WAS ABLE TO SHOW TWO ADDITIONAL RESULTS IN THE PSEUDO-SOLUTION TO THE X-RAY DATA OF 1E94SF DIFFERENT FROM THE ORIGINAL AUTHORS. (1). THE BOUND NUCLEOTIDE WAS ADP IN AN ANTI CONFORMATION, NOT AS THE ORIGINAL AUTHORS CLAIMED THAT THE NUCLEOTIDE WAS AMPPNP IN A SYN CONFORMATION. THIS FINDING AGREES WITH REFERENCES 3 AND 4 IN NUCLEOTIDE CONFORMATION AND HSLU CONFORMATION. (2). THE BIOLOGICALLY RELEVANT HSLVU COMPLEX WAS CLEARLY PRESENT IN THE X-RAY DIFFRACTION DATA, IN WHICH HSLU SUBUNITS E AND F WERE TRANSLATED BY 158 ANGSTRONMS IN ASYMMETRIC UNIT. THIS COMPLEX CONTRIBUTED ABOUT 8% OF THE OBSERVED 1E94 INTENSITY DATA.
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 32.13 Å2 / ksol: 0.326 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 70.2 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: 2.8→29.62 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.8→2.98 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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