+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7azp | |||||||||
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タイトル | Structure of the human mitochondrial HSPD1 single ring | |||||||||
要素 | 60 kDa heat shock protein, mitochondrial | |||||||||
キーワード | CHAPERONE / HSPD1 / Hsp60 / chaperonin | |||||||||
機能・相同性 | 機能・相同性情報 coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / lipopolysaccharide receptor complex / protein import into mitochondrial intermembrane space / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell ...coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / lipopolysaccharide receptor complex / protein import into mitochondrial intermembrane space / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell / Mitochondrial protein import / chaperonin ATPase / positive regulation of macrophage activation / cellular response to interleukin-7 / MyD88-dependent toll-like receptor signaling pathway / biological process involved in interaction with symbiont / 'de novo' protein folding / sperm plasma membrane / B cell proliferation / B cell activation / apolipoprotein binding / DNA replication origin binding / positive regulation of interferon-alpha production / apoptotic mitochondrial changes / protein maturation / positive regulation of interleukin-10 production / response to unfolded protein / chaperone-mediated protein complex assembly / clathrin-coated pit / sperm midpiece / positive regulation of interleukin-12 production / Mitochondrial protein degradation / response to cold / T cell activation / secretory granule / isomerase activity / lipopolysaccharide binding / ATP-dependent protein folding chaperone / : / positive regulation of interleukin-6 production / positive regulation of type II interferon production / double-stranded RNA binding / positive regulation of T cell activation / unfolded protein binding / p53 binding / protein folding / single-stranded DNA binding / protein-folding chaperone binding / protein refolding / mitochondrial inner membrane / early endosome / protein stabilization / mitochondrial matrix / positive regulation of apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol / cytoplasm 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 | Klebl, D.P. / Feasey, M.C. / Muench, S.P. | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: iScience / 年: 2021 タイトル: Cryo-EM structure of human mitochondrial HSPD1. 著者: David P Klebl / Matthew C Feasey / Emma L Hesketh / Neil A Ranson / Heiko Wurdak / Frank Sobott / Robin S Bon / Stephen P Muench / 要旨: Chaperonins play an important role in folding newly synthesized or translocated proteins in all organisms. The bacterial chaperonin GroEL has served as a model system for the understanding of these ...Chaperonins play an important role in folding newly synthesized or translocated proteins in all organisms. The bacterial chaperonin GroEL has served as a model system for the understanding of these proteins. In comparison, its human homolog, known as mitochondrial heat shock protein family member D1 (HSPD1) is poorly understood. Here, we present the structure of HSPD1 in the apo state determined by cryo-electron microscopy (cryo-EM). Unlike GroEL, HSPD1 forms mostly single ring assemblies in the absence of co-chaperonin (HSPE1). Comparison with GroEL shows a rotation and increased flexibility of the apical domain. Together with published structures of the HSPD1/HSPE1 co-chaperonin complex, this work gives insight into the structural changes that occur during the catalytic cycle. This new understanding of HSPD1 structure and its rearrangements upon complex formation may provide new insights for the development of HSPD1-targeting treatments against a diverse range of diseases including glioblastoma. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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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 | 7azp.cif.gz | 585.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7azp.ent.gz | 491.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7azp.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 | 7azp_validation.pdf.gz | 1.1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7azp_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | 7azp_validation.xml.gz | 102.9 KB | 表示 | |
CIF形式データ | 7azp_validation.cif.gz | 155.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/az/7azp ftp://data.pdbj.org/pub/pdb/validation_reports/az/7azp | HTTPS FTP |
-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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-要素
#1: タンパク質 | 分子量: 58306.977 Da / 分子数: 7 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HSPD1, HSP60 / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: P10809, chaperonin ATPase |
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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: human mitochondrial heat shock protein family member D1 (HSPD1) タイプ: COMPLEX 詳細: produced by heterologous expression, mature HSPD1, apo state Entity ID: all / 由来: RECOMBINANT |
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分子量 | 実験値: NO |
由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Escherichia coli (大腸菌) |
緩衝液 | pH: 7.7 |
試料 | 濃度: 2.3 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 90 % / 凍結前の試料温度: 293 K / 詳細: blot time 6 s blot force 6 |
-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 |
撮影 | 平均露光時間: 70 sec. / 電子線照射量: 38.5 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 撮影したグリッド数: 1 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.17.1_3660: / 分類: 精密化 | |||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 124784 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||
原子モデル構築 | プロトコル: OTHER / 空間: REAL | |||||||||||||||||||||||||||
原子モデル構築 |
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拘束条件 |
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