[日本語] English
万見
- EMDB-3338: Atomic cryoEM structure of Hsp90/Cdc37/Cdk4 complex -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: EMDB / ID: EMD-3338
タイトルAtomic cryoEM structure of Hsp90/Cdc37/Cdk4 complex
マップデータReconstruction of Hsp90:Cdc37:Cdk4 complex. Part of series of maps, the highest resolution map being EMD-3337, but this one having better density coiled coil in Cdc37.
試料
  • 試料: Complex of Human Hsp90 beta, human Cdc37 and human Cdk4
  • タンパク質・ペプチド: Heat Shock Protein HSP 90 beta
  • タンパク質・ペプチド: Hsp90 co-chaperone Cdc37
  • タンパク質・ペプチド: Cyclin-dependent kinase 4
キーワードHsp90 / Cdc37 / Cdk4 / chaperone / kinase / unfolding
機能・相同性
機能・相同性情報


cyclin D3-CDK4 complex / cyclin D1-CDK4 complex / cyclin D2-CDK4 complex / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 / cellular response to ionomycin / citrulline metabolic process / regulation of transcription initiation by RNA polymerase II / Drug-mediated inhibition of CDK4/CDK6 activity / regulation of type II interferon-mediated signaling pathway ...cyclin D3-CDK4 complex / cyclin D1-CDK4 complex / cyclin D2-CDK4 complex / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 / cellular response to ionomycin / citrulline metabolic process / regulation of transcription initiation by RNA polymerase II / Drug-mediated inhibition of CDK4/CDK6 activity / regulation of type II interferon-mediated signaling pathway / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / regulation of type B pancreatic cell proliferation / HSP90-CDC37 chaperone complex / very long-chain fatty acid metabolic process / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / dynein axonemal particle / histone methyltransferase binding / Transcriptional regulation by RUNX2 / mitochondrial genome maintenance / cellular response to phorbol 13-acetate 12-myristate / receptor ligand inhibitor activity / positive regulation of type 2 mitophagy / ATP-dependent protein binding / positive regulation of protein localization to cell surface / protein kinase regulator activity / protein folding chaperone complex / cyclin-dependent protein serine/threonine kinase regulator activity / post-transcriptional regulation of gene expression / regulation of cyclin-dependent protein serine/threonine kinase activity / Respiratory syncytial virus genome replication / positive regulation of transforming growth factor beta receptor signaling pathway / telomerase holoenzyme complex assembly / PTK6 Regulates Cell Cycle / Uptake and function of diphtheria toxin / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / regulation of type I interferon-mediated signaling pathway / TPR domain binding / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / Assembly and release of respiratory syncytial virus (RSV) virions / dendritic growth cone / The NLRP3 inflammasome / protein phosphatase activator activity / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / HSF1-dependent transactivation / bicellular tight junction / response to unfolded protein / cyclin-dependent kinase / HSF1 activation / telomere maintenance via telomerase / cyclin-dependent protein serine/threonine kinase activity / protein targeting / chaperone-mediated protein complex assembly / Attenuation phase / Purinergic signaling in leishmaniasis infection / RHOBTB2 GTPase cycle / axonal growth cone / cyclin-dependent protein kinase holoenzyme complex / DNA polymerase binding / supramolecular fiber organization / : / regulation of G2/M transition of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / heat shock protein binding / Signaling by ERBB2 / protein folding chaperone / nitric-oxide synthase regulator activity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cyclin binding / cellular response to interleukin-4 / peptide binding / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / Ubiquitin-dependent degradation of Cyclin D / positive regulation of cell differentiation / placenta development / Hsp90 protein binding / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / tau protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Oncogene Induced Senescence / Signaling by ERBB2 KD Mutants / Transcriptional regulation of white adipocyte differentiation / Meiotic recombination
類似検索 - 分子機能
Cdc37, C-terminal / Cdc37, Hsp90 binding / Cdc37, Hsp90-binding domain superfamily / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 N terminal kinase binding / Cdc37 / Cdc37, N-terminal domain ...Cdc37, C-terminal / Cdc37, Hsp90 binding / Cdc37, Hsp90-binding domain superfamily / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 N terminal kinase binding / Cdc37 / Cdc37, N-terminal domain / Cdc37 N terminal kinase binding / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / : / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
Heat shock protein HSP 90-beta / Cyclin-dependent kinase 4 / Hsp90 co-chaperone Cdc37
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.0 Å
データ登録者Verba KA / Wang RYR / Arakawa A / Liu Y / Shirouzu M / Yokoyama S / Agard DA
引用ジャーナル: Science / 年: 2016
タイトル: Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase.
著者: Kliment A Verba / Ray Yu-Ruei Wang / Akihiko Arakawa / Yanxin Liu / Mikako Shirouzu / Shigeyuki Yokoyama / David A Agard /
要旨: The Hsp90 molecular chaperone and its Cdc37 cochaperone help stabilize and activate more than half of the human kinome. However, both the mechanism by which these chaperones assist their "client" ...The Hsp90 molecular chaperone and its Cdc37 cochaperone help stabilize and activate more than half of the human kinome. However, both the mechanism by which these chaperones assist their "client" kinases and the reason why some kinases are addicted to Hsp90 while closely related family members are independent are unknown. Our structural understanding of these interactions is lacking, as no full-length structures of human Hsp90, Cdc37, or either of these proteins with a kinase have been elucidated. Here we report a 3.9 angstrom cryo-electron microscopy structure of the Hsp90-Cdc37-Cdk4 kinase complex. Surprisingly, the two lobes of Cdk4 are completely separated with the β4-β5 sheet unfolded. Cdc37 mimics part of the kinase N lobe, stabilizing an open kinase conformation by wedging itself between the two lobes. Finally, Hsp90 clamps around the unfolded kinase β5 strand and interacts with exposed N- and C-lobe interfaces, protecting the kinase in a trapped unfolded state. On the basis of this structure and an extensive amount of previously collected data, we propose unifying conceptual and mechanistic models of chaperone-kinase interactions.
履歴
登録2016年2月18日-
ヘッダ(付随情報) 公開2016年3月9日-
マップ公開2016年6月29日-
更新2016年7月20日-
現状2016年7月20日処理サイト: PDBe / 状態: 公開

-
構造の表示

ムービー
  • 表面図（断面を密度値に従い着色）
  • 表面レベル: 0.015
  • UCSF Chimeraによる作画
  • ダウンロード
  • 表面図（半径に従い着色）
  • 表面レベル: 0.015
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
構造ビューアEMマップ:
SurfViewMolmilJmol/JSmol
添付画像

emd_3338.tif

ダウンロードとリンク

-
マップ

ファイルダウンロード / ファイル: emd_3338.map.gz / 形式: CCP4 / 大きさ: 62.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈Reconstruction of Hsp90:Cdc37:Cdk4 complex. Part of series of maps, the highest resolution map being EMD-3337, but this one having better density coiled coil in Cdc37.
投影像・断面図

画像のコントロール

大きさ
明度
コントラスト
その他
軸Z (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 256 pix.
= 336.64 Å		1.32 Å/pix.
x 256 pix.
= 336.64 Å		1.32 Å/pix.
x 256 pix.
= 336.64 Å

表面

投影像

断面 (1/3)

断面 (1/2)

断面 (2/3)

画像は Spider により作成

ボクセルのサイズX=Y=Z: 1.315 Å
密度

ヒストグラム

ヒストグラム (対数)
表面レベル登録者による: 0.015 / ムービー #1: 0.015
最小 - 最大-0.02610713 - 0.07158083
平均 (標準偏差)0.00003204 (±0.00188652)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ256256256
Spacing256256256
セルA=B=C: 336.64 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.3151.3151.315
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z336.640336.640336.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0260.0720.000

-
添付データ

-
試料の構成要素

-
全体 : Complex of Human Hsp90 beta, human Cdc37 and human Cdk4

全体名称: Complex of Human Hsp90 beta, human Cdc37 and human Cdk4
要素
  • 試料: Complex of Human Hsp90 beta, human Cdc37 and human Cdk4
  • タンパク質・ペプチド: Heat Shock Protein HSP 90 beta
  • タンパク質・ペプチド: Hsp90 co-chaperone Cdc37
  • タンパク質・ペプチド: Cyclin-dependent kinase 4

-
超分子 #1000: Complex of Human Hsp90 beta, human Cdc37 and human Cdk4

超分子名称: Complex of Human Hsp90 beta, human Cdc37 and human Cdk4
タイプ: sample / ID: 1000 / 詳細: All three proteins were co-expressed in Sf9 cells.
集合状態: One Hsp90 homodimer binds to one Cdc37 and one Cdk4
Number unique components: 3
分子量実験値: 245 KDa / 理論値: 245 KDa / 手法: As cloned, verified by SDS-PAGE

-
分子 #1: Heat Shock Protein HSP 90 beta

分子名称: Heat Shock Protein HSP 90 beta / タイプ: protein_or_peptide / ID: 1 / Name.synonym: Hsp90 / コピー数: 2 / 集合状態: Dimer / 組換発現: Yes
由来(天然)生物種: Homo sapiens (ヒト) / 別称: Human / 細胞中の位置: cytoplasm
分子量理論値: 83 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
組換プラスミド: pFastBacHT
配列UniProtKB: Heat shock protein HSP 90-beta / GO: citrulline metabolic process / InterPro: Heat shock protein Hsp90 family

-
分子 #2: Hsp90 co-chaperone Cdc37

分子名称: Hsp90 co-chaperone Cdc37 / タイプ: protein_or_peptide / ID: 2 / Name.synonym: Cdc37 / コピー数: 1 / 組換発現: Yes
由来(天然)生物種: Homo sapiens (ヒト) / 別称: Human / 細胞中の位置: throughout
分子量理論値: 44.5 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
組換プラスミド: pFastBacHT
配列UniProtKB: Hsp90 co-chaperone Cdc37 / GO: mitochondrial genome maintenance

-
分子 #3: Cyclin-dependent kinase 4

分子名称: Cyclin-dependent kinase 4 / タイプ: protein_or_peptide / ID: 3 / Name.synonym: Cdk4 / コピー数: 1 / 組換発現: Yes
由来(天然)生物種: Homo sapiens (ヒト) / 別称: Human / 細胞中の位置: throughout
分子量理論値: 33.7 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
組換プラスミド: pFastBacHT
配列UniProtKB: Cyclin-dependent kinase 4 / GO: very long-chain fatty acid metabolic process / InterPro: Protein kinase domain

-
実験情報

-
構造解析

手法クライオ電子顕微鏡法
解析単粒子再構成法
試料の集合状態particle

-
試料調製

濃度0.27 mg/mL
緩衝液pH: 7.5
詳細: 20mM Tris-HCl (pH 7.5), 150 mM NaCl, 10 mM KCl, 10 mM MgCl2, 20 mM Na2MoO4, 2mM DTT, 0.085mM DDM
グリッド詳細: Glow discharged for 30 sec, C-flat 400 mesh 1.2/1.3 thick carbon grids (Protochips)
凍結凍結剤: ETHANE / チャンバー内湿度: 90 % / チャンバー内温度: 95 K / 装置: FEI VITROBOT MARK III / 手法: Single blot from 4 to 6 seconds, at 20C

-
電子顕微鏡法

顕微鏡FEI TITAN KRIOS
アライメント法Legacy - 非点収差: At high mag via FT.
日付2014年11月25日
撮影カテゴリ: CCD
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)
実像数: 3718 / 平均電子線量: 44 e/Å2 / 詳細: 38 frames, 7.6 seconds total exposure / ビット/ピクセル: 8
電子線加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN
電子光学系照射モード: OTHER / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス（公称値）: 3.8 µm / 最小 デフォーカス（公称値）: 1.4 µm / 倍率（公称値）: 22500
試料ステージ試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
実験機器
モデル: Titan Krios / 画像提供: FEI Company

-
画像解析

詳細Image stacks were corrected for motion and summed as described previously, resulting in binned sums (1.315A/pix). For particle picking the images were binned to 5.2A/pix and Gaussian bandpass filtered between 15A and 500A using EMAN2. SamViewer template based picking was then used to pick particles from all the micrographs, followed by manual review of all the picks. After such procedure 802877 particles were picked in total and extracted from images binned to 2.6A/pix. CTFFIND4 was used to estimate defocus parameters for all the images. Relion 1.4 was used for all the following steps unless noted otherwise. Reference free 2D classification into 300 classes for 75 iterations was performed followed by manual examination of the resulting class averages. Low resolution/signal to noise/feature class averages and contributing particles were discarded, resulting in 670000 particles left. The resulting particles were 3D classified into 4 classes resulting in two classes having high-resolution features (390000 particles). At this stage particles were extracted from 1.315A/pix micrographs and all the following processing was done with these particles. Using 3D Auto-refine in Relion 1.4, a reconstruction was obtained from 390000 particles resulting from 3D classification above (using highest resolution 3D class as initial model, low pass filtered to 20A). Using the resulting parameters, the particles were further drift corrected per particle and dose weighted using the Particle Polishing feature. The B-factor weighing curve was fit by a polynomial (with a rationale that such a curve should be smooth) and used to generate new weighting parameters for Particle Polishing, with which 390000 particles were then polished. All further data processing was done using the polished particles. Re-refinement of the 390000 particles after polishing yielded the map at about 4A resolution (determined using gold standard FSC in the PostProcessing tab). Raw particles were sharpened with a B-factor of -50, low pass filtered with Gaussian filter to 3A and the refinement was continued for 10 more iterations (until convergence) with these particles (the rationale was that due to extremely low noise levels of K2 direct detector, this would yield more accurate alignments due to presence of more high resolution data in the images). This resulted in similar resolution but one with visually sharper features.
最終 再構成想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 4.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Relion / 使用した粒子像数: 388688
最終 2次元分類クラス数: 1
FSC曲線 (解像度の算出)

-
原子モデル構築 1

初期モデルPDB ID:

5fwk


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: E / Chain - #3 - Chain ID: K
ソフトウェア名称: Chimera
詳細The model was built using Rosetta into this map and its sister EMD-3337(depending on the region), but was refined into the EMD-3337 map only. Then the resulting model was rigid body fit into this map in Chimera.
精密化空間: REAL / プロトコル: RIGID BODY FIT

+
万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

+
2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る