+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5a0q | ||||||
---|---|---|---|---|---|---|---|
タイトル | Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core | ||||||
要素 |
| ||||||
キーワード | HYDROLASE / PROTEASOME / 20S / ADAAHX3L3VS / LIGAND / INHIBITOR / DRUG DESIGN | ||||||
機能・相同性 | 機能・相同性情報 purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex ...purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / negative regulation of inflammatory response to antigenic stimulus / : / sarcomere / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / proteolysis involved in protein catabolic process / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / lipopolysaccharide binding / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / P-body / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Orc1 removal from chromatin / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / response to virus / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / response to organic cyclic compound / CLEC7A (Dectin-1) signaling / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / nuclear matrix / Regulation of PTEN stability and activity / Interleukin-1 signaling / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / regulation of inflammatory response / Downstream TCR signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / positive regulation of NF-kappaB transcription factor activity / peptidase activity / ER-Phagosome pathway / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / response to oxidative stress / ficolin-1-rich granule lumen / postsynapse / nuclear body / ribosome / Ub-specific processing proteases / cadherin binding / intracellular membrane-bounded organelle / centrosome / ubiquitin protein ligase binding / synapse / Neutrophil degranulation / mitochondrion / proteolysis / RNA binding 類似検索 - 分子機能 | ||||||
生物種 | HOMO SAPIENS (ヒト) | ||||||
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: 3.5 Å | ||||||
データ登録者 | daFonseca, P.C.A. / Morris, E.P. | ||||||
引用 | ジャーナル: Nat Commun / 年: 2015 タイトル: Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core. 著者: Paula C A da Fonseca / Edward P Morris / 要旨: The proteasome is a highly regulated protease complex fundamental for cell homeostasis and controlled cell cycle progression. It functions by removing a wide range of specifically tagged proteins, ...The proteasome is a highly regulated protease complex fundamental for cell homeostasis and controlled cell cycle progression. It functions by removing a wide range of specifically tagged proteins, including key cellular regulators. Here we present the structure of the human 20S proteasome core bound to a substrate analogue inhibitor molecule, determined by electron cryo-microscopy (cryo-EM) and single-particle analysis at a resolution of around 3.5 Å. Our map allows the building of protein coordinates as well as defining the location and conformation of the inhibitor at the different active sites. These results open new prospects to tackle the proteasome functional mechanisms. Moreover, they also further demonstrate that cryo-EM is emerging as a realistic approach for general structural studies of protein-ligand interactions. | ||||||
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 | 5a0q.cif.gz | 936.6 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb5a0q.ent.gz | 759 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5a0q.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 | 5a0q_validation.pdf.gz | 1.4 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 5a0q_full_validation.pdf.gz | 1.4 MB | 表示 | |
XML形式データ | 5a0q_validation.xml.gz | 136 KB | 表示 | |
CIF形式データ | 5a0q_validation.cif.gz | 211.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/a0/5a0q ftp://data.pdbj.org/pub/pdb/validation_reports/a0/5a0q | HTTPS FTP |
-関連構造データ
関連構造データ | 2981MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
---|---|
類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10038 (タイトル: Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core Data size: 579.1 Data #1: raw micrographs of the human 20S proteasome core complex bound to the ligand AdaAhx3L3VS [micrographs - multiframe]) |
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
-PROTEASOME SUBUNIT ALPHA TYPE- ... , 7種, 14分子 AOBPCQDRESFTGU
#1: タンパク質 | 分子量: 27432.459 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / Cell: ERYTHROCYTES / 参照: UniProt: P60900, proteasome endopeptidase complex #2: タンパク質 | 分子量: 25927.535 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / Cell: ERYTHROCYTES / 参照: UniProt: P25787, proteasome endopeptidase complex #3: タンパク質 | 分子量: 29525.842 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / Cell: ERYTHROCYTES / 参照: UniProt: P25789, proteasome endopeptidase complex #4: タンパク質 | 分子量: 27929.891 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / Cell: ERYTHROCYTES / 参照: UniProt: O14818, proteasome endopeptidase complex #5: タンパク質 | 分子量: 26435.977 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / Cell: ERYTHROCYTES / 参照: UniProt: P28066, proteasome endopeptidase complex #6: タンパク質 | 分子量: 29595.627 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / Cell: ERYTHROCYTES / 参照: UniProt: P25786, proteasome endopeptidase complex #7: タンパク質 | 分子量: 28469.252 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / Cell: ERYTHROCYTES / 参照: UniProt: P25788, proteasome endopeptidase complex |
---|
-PROTEASOME SUBUNIT BETA TYPE- ... , 7種, 14分子 HVIWJXKYLZMaNb
#8: タンパク質 | 分子量: 21921.836 Da / 分子数: 2 / 由来タイプ: 天然 詳細: SUBUNIT PARTIALLY BOUND TO THE INHIBITOR ADAMANTANE-ACETYL-(6-AMINOHEXANOYL)3-(LEUCINYL)3-VINYL-(METHYL)-SULFONE (ADAAHX3L3VS) 由来: (天然) HOMO SAPIENS (ヒト) / Cell: ERYTHROCYTES / 参照: UniProt: P28072, proteasome endopeptidase complex #9: タンパク質 | 分子量: 25321.980 Da / 分子数: 2 / 由来タイプ: 天然 詳細: SUBUNIT PARTIALLY BOUND TO THE INHIBITOR ADAMANTANE-ACETYL-(6-AMINOHEXANOYL)3-(LEUCINYL)3-VINYL-(METHYL)-SULFONE (ADAAHX3L3VS) 由来: (天然) HOMO SAPIENS (ヒト) / Cell: ERYTHROCYTES / 参照: UniProt: Q99436, proteasome endopeptidase complex #10: タンパク質 | 分子量: 22841.701 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / Cell: ERYTHROCYTES / 参照: UniProt: P49720, proteasome endopeptidase complex #11: タンパク質 | 分子量: 22864.277 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / Cell: ERYTHROCYTES / 参照: UniProt: P49721, proteasome endopeptidase complex #12: タンパク質 | 分子量: 22484.369 Da / 分子数: 2 / 由来タイプ: 天然 詳細: SUBUNIT BOUND TO THE INHIBITOR ADAMANTANE-ACETYL-(6-AMINOHEXANOYL)3-(LEUCINYL)3-VINYL-(METHYL)-SULFONE (ADAAHX3L3VS) 由来: (天然) HOMO SAPIENS (ヒト) / Cell: ERYTHROCYTES / 参照: UniProt: P28074, proteasome endopeptidase complex #13: タンパク質 | 分子量: 23578.986 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / Cell: ERYTHROCYTES / 参照: UniProt: P20618, proteasome endopeptidase complex #14: タンパク質 | 分子量: 24414.740 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / Cell: ERYTHROCYTES / 参照: UniProt: P28070, proteasome endopeptidase complex |
---|
-非ポリマー , 1種, 6分子
#15: 化合物 | ChemComp-KNM / |
---|
-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: HUMAN 20S PROTEASOME CORE / タイプ: COMPLEX 詳細: THE POWER SPECTRA OF THE IMAGES SELECTED FOR ANALYSIS HAD ISOTROPIC THON RINGS DIRECTLY OBSERVED TO 4 ANGSTROMS OR BETTER |
---|---|
緩衝液 | 名称: 50 MM TRIS-HCL, 5 MM MGCL2 AND 1MM DITHIOTREITOL / pH: 7.5 / 詳細: 50 MM TRIS-HCL, 5 MM MGCL2 AND 1MM DITHIOTREITOL |
試料 | 濃度: 0.1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: CARBON |
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: ETHANE 詳細: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT 2. 5 SECONDS BEFORE PLUNGING, |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS / 日付: 2014年2月4日 詳細: EACH EXPOSURE WAS RECORDED AS 17 INDIVIDUAL FRAMES CAPTURED AT A RATE OF 0.056 SECONDS PER FRAME, WITH AN ELECTRON DOSE OF 2.8 ELECTRONS PER SQUARE ANGSTROM. DATA-SET RECORDED USING EPU SOFTWARE. |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 75000 X / 倍率(補正後): 134461 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): 1700 nm / Cs: 2.7 mm |
試料ホルダ | 温度: 85 K |
撮影 | 電子線照射量: 4.8 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
画像スキャン | デジタル画像の数: 960 |
-解析
EMソフトウェア |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | 詳細: FULL RECORDED IMAGE | ||||||||||||||||||
対称性 | 点対称性: C2 (2回回転対称) | ||||||||||||||||||
3次元再構成 | 手法: PROJECTION MATCHING / 解像度: 3.5 Å / 粒子像の数: 76500 / ピクセルサイズ(実測値): 1.04 Å 詳細: DISORDERED REGIONS, NOT RECOVERED IN THE EM MAP, WHERE NOT MODELED. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2981. (DEPOSITION ID: 13310). 対称性のタイプ: POINT | ||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL / 詳細: METHOD--FLEXIBLE | ||||||||||||||||||
原子モデル構築 | PDB-ID: 3UNE | ||||||||||||||||||
精密化 | 最高解像度: 3.5 Å | ||||||||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 3.5 Å
|