+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8xj4 | ||||||
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タイトル | Structure of prostatic acid phosphatase in human semen | ||||||
要素 | Prostatic acid phosphatase | ||||||
キーワード | CELL CYCLE / Acid phosphatase | ||||||
機能・相同性 | 機能・相同性情報 thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / lysophosphatidic acid phosphatase activity / XMP 5'-nucleosidase activity / acid phosphatase activity ...thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / lysophosphatidic acid phosphatase activity / XMP 5'-nucleosidase activity / acid phosphatase activity / 5'-nucleotidase / 5'-nucleotidase activity / vesicle membrane / nucleotide metabolic process / choline binding / azurophil granule membrane / lysosome organization / phosphatase activity / purine nucleobase metabolic process / dephosphorylation / multivesicular body / protein-tyrosine-phosphatase / filopodium / protein tyrosine phosphatase activity / lipid metabolic process / apical part of cell / molecular adaptor activity / lysosome / lysosomal membrane / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol 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: 3.19 Å | ||||||
データ登録者 | Liu, X.Z. / Li, J.L. / Deng, D. / Wang, X. | ||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Biochem Biophys Res Commun / 年: 2024 タイトル: Purification, identification and Cryo-EM structure of prostatic acid phosphatase in human semen. 著者: Xuanzhong Liu / Lin Yu / Zhili Xia / Jialu Li / Wenbo Meng / Ling Min / Fuping Li / Xiang Wang / 要旨: Prostatic acid phosphatase (PAP) is a glycoprotein that plays a crucial role in the hydrolysis of phosphate ester present in prostatic exudates. It is a well-established indicator for prostate cancer ...Prostatic acid phosphatase (PAP) is a glycoprotein that plays a crucial role in the hydrolysis of phosphate ester present in prostatic exudates. It is a well-established indicator for prostate cancer due to its elevated serum levels in disease progression. Despite its abundance in semen, PAP's influence on male fertility has not been extensively studied. In our study, we report a significantly optimized method for purifying human endogenous PAP, achieving remarkably high efficiency and active protein recovery rate. This achievement allowed us to better analyze and understand the PAP protein. We determined the cryo-electron microscopic (Cryo-EM) structure of prostatic acid phosphatase in its physiological state for the first time. Our structural and gel filtration analysis confirmed the formation of a tight homodimer structure of human PAP. This functional homodimer displayed an elongated conformation in the cryo-EM structure compared to the previously reported crystal structure. Additionally, there was a notable 5-degree rotation in the angle between the α domain and α/β domain of each monomer. Through structural analysis, we revealed three potential glycosylation sites: Asn94, Asn220, and Asn333. These sites contained varying numbers and forms of glycosyl units, suggesting sugar moieties influence PAP function. Furthermore, we found that the active sites of PAP, His44 and Asp290, are located between the two protein domains. Overall, our study not only provide an optimized approach for PAP purification, but also offer crucial insights into its structural characteristics. These findings lay the groundwork for further investigations into the physiological function and potential therapeutic applications of this important protein. | ||||||
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 | 8xj4.cif.gz | 138.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8xj4.ent.gz | 107.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8xj4.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 | 8xj4_validation.pdf.gz | 1.5 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8xj4_full_validation.pdf.gz | 1.5 MB | 表示 | |
XML形式データ | 8xj4_validation.xml.gz | 33.3 KB | 表示 | |
CIF形式データ | 8xj4_validation.cif.gz | 47.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/xj/8xj4 ftp://data.pdbj.org/pub/pdb/validation_reports/xj/8xj4 | HTTPS FTP |
-関連構造データ
関連構造データ | 38393MC 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) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 40262.949 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 組織: Human seminal plasma 参照: UniProt: P15309, acid phosphatase, 5'-nucleotidase, protein-tyrosine-phosphatase #2: 多糖 | alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #3: 多糖 | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | タイプ: oligosaccharide / 分子量: 748.682 Da / 分子数: 1 / 由来タイプ: 合成 #4: 糖 | ChemComp-NAG / #5: 糖 | ChemComp-MAN / | 研究の焦点であるリガンドがあるか | Y | |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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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: structure of prostatic acid phosphatase in human semen タイプ: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / 由来: NATURAL |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
緩衝液 | pH: 8 |
試料 | 濃度: 8.5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
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 / 最大 デフォーカス(公称値): 1800 nm / 最小 デフォーカス(公称値): 1200 nm |
撮影 | 電子線照射量: 50 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
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3次元再構成 | 解像度: 3.19 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 75346 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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