+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5w0s | ||||||
---|---|---|---|---|---|---|---|
タイトル | GroEL using cryoEM | ||||||
要素 | 60 kDa chaperonin | ||||||
キーワード | CHAPERONE / GroEL / cryoEM / conformational heterogeneity. | ||||||
機能・相同性 | 機能・相同性情報 GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein refolding ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein refolding / response to heat / magnesium ion binding / ATP hydrolysis activity / 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 | 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 | Roh, S.H. / Chiu, W. | ||||||
資金援助 | 米国, 1件
| ||||||
引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2017 タイトル: Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM. 著者: Soung-Hun Roh / Corey F Hryc / Hyun-Hwan Jeong / Xue Fei / Joanita Jakana / George H Lorimer / Wah Chiu / 要旨: Single-particle electron cryo-microscopy (cryo-EM) is an emerging tool for resolving structures of conformationally heterogeneous particles; however, each structure is derived from an average of many ...Single-particle electron cryo-microscopy (cryo-EM) is an emerging tool for resolving structures of conformationally heterogeneous particles; however, each structure is derived from an average of many particles with presumed identical conformations. We used a 3.5-Å cryo-EM reconstruction with imposed D7 symmetry to further analyze structural heterogeneity among chemically identical subunits in each GroEL oligomer. Focused classification of the 14 subunits in each oligomer revealed three dominant classes of subunit conformations. Each class resembled a distinct GroEL crystal structure in the Protein Data Bank. The conformational differences stem from the orientations of the apical domain. We mapped each conformation class to its subunit locations within each GroEL oligomer in our dataset. The spatial distributions of each conformation class differed among oligomers, and most oligomers contained 10-12 subunits of the three dominant conformation classes. Adjacent subunits were found to more likely assume the same conformation class, suggesting correlation among subunits in the oligomer. This study demonstrates the utility of cryo-EM in revealing structure dynamics within a single protein oligomer. | ||||||
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 | 5w0s.cif.gz | 1.7 MB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb5w0s.ent.gz | 1.3 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5w0s.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 | 5w0s_validation.pdf.gz | 1.4 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 5w0s_full_validation.pdf.gz | 1.5 MB | 表示 | |
XML形式データ | 5w0s_validation.xml.gz | 187.8 KB | 表示 | |
CIF形式データ | 5w0s_validation.cif.gz | 305.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/w0/5w0s ftp://data.pdbj.org/pub/pdb/validation_reports/w0/5w0s | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
モデル数 | 4 |
-要素
#1: タンパク質 | 分子量: 55148.020 Da / 分子数: 14 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: mopA, groEL, groL / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q6Q099, UniProt: P0A6F5*PLUS #2: 水 | ChemComp-HOH / | |
---|
-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: Wild type GroEL / タイプ: COMPLEX / Entity ID: #1 / 由来: RECOMBINANT |
---|---|
分子量 | 値: 800 kDa/nm / 実験値: NO |
由来(天然) | 生物種: Escherichia coli (大腸菌) |
由来(組換発現) | 生物種: Escherichia coli (大腸菌) |
緩衝液 | pH: 7.2 |
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 |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
顕微鏡 | モデル: JEOL 3200FSC |
---|---|
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 | 電子線照射量: 1 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
EMソフトウェア | 名称: RELION / バージョン: 1.4 / カテゴリ: 3次元再構成 |
---|---|
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
対称性 | 点対称性: D7 (2回x7回 2面回転対称) |
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: 37367 / 対称性のタイプ: POINT |
原子モデル構築 | 詳細: Regarding negative occupancies: To assess fit-to-density, we derived cross-correlations at the amino acid level and by means of a map/model FSC. To perform this assessment, we generated a ...詳細: Regarding negative occupancies: To assess fit-to-density, we derived cross-correlations at the amino acid level and by means of a map/model FSC. To perform this assessment, we generated a weighted map, derived solely from an atomic model that accounted for both ADP of all atoms and weak/negative density of all charged oxygen atoms, and compared it with the experimental map. The weighted map provides a better approximation of the experimental map by simulating map variability as opposed to treating all atoms equally. The correlations for both the FSC and the per-residue assessment showed improvements when properly weighted, further demonstrating that our model provides a good approximation of the experimental data |