- EMDB-5609: Structural dynamics and inter-ring communication of the MecA-ClpC... -
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基本情報
登録情報
データベース: EMDB / ID: EMD-5609
タイトル
Structural dynamics and inter-ring communication of the MecA-ClpC complex during active substrate unfolding and translocation revealed by cryo-EM
マップデータ
Reconstruction of MecA-ClpC(E280A,E618A) complex with ATP state
試料
試料: MecA-ClpC (E280A,E618A) with ATP
タンパク質・ペプチド: MecA
タンパク質・ペプチド: ClpC
キーワード
unfolding / AAA+ ATPase / MecA / ClpC
機能・相同性
機能・相同性情報
negative regulation of establishment of competence for transformation / negative regulation of sporulation resulting in formation of a cellular spore / establishment of competence for transformation / sporulation resulting in formation of a cellular spore / protein-macromolecule adaptor activity / ATP hydrolysis activity / ATP binding 類似検索 - 分子機能
MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / : / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. ...MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / : / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase 類似検索 - ドメイン・相同性
Negative regulator of genetic competence ClpC/MecB / Adapter protein MecA 1 類似検索 - 構成要素
ジャーナル: J Biol Chem / 年: 2013 タイトル: Structural dynamics of the MecA-ClpC complex: a type II AAA+ protein unfolding machine. 著者: Jing Liu / Ziqing Mei / Ningning Li / Yutao Qi / Yanji Xu / Yigong Shi / Feng Wang / Jianlin Lei / Ning Gao / 要旨: The MecA-ClpC complex is a bacterial type II AAA(+) molecular machine responsible for regulated unfolding of substrates, such as transcription factors ComK and ComS, and targeting them to ClpP for ...The MecA-ClpC complex is a bacterial type II AAA(+) molecular machine responsible for regulated unfolding of substrates, such as transcription factors ComK and ComS, and targeting them to ClpP for degradation. The six subunits of the MecA-ClpC complex form a closed barrel-like structure, featured with three stacked rings and a hollow passage, where substrates are threaded and translocated through successive pores. Although the general concepts of how polypeptides are unfolded and translocated by internal pore loops of AAA(+) proteins have long been conceived, the detailed mechanistic model remains elusive. With cryoelectron microscopy, we captured four different structures of the MecA-ClpC complexes. These complexes differ in the nucleotide binding states of the two AAA(+) rings and therefore might presumably reflect distinctive, representative snapshots from a dynamic unfolding cycle of this hexameric complex. Structural analysis reveals that nucleotide binding and hydrolysis modulate the hexameric complex in a number of ways, including the opening of the N-terminal ring, the axial and radial positions of pore loops, the compactness of the C-terminal ring, as well as the relative rotation between the two nucleotide-binding domain rings. More importantly, our structural and biochemical data indicate there is an active allosteric communication between the two AAA(+) rings and suggest that concerted actions of the two AAA(+) rings are required for the efficiency of the substrate unfolding and translocation. These findings provide important mechanistic insights into the dynamic cycle of the MecA-ClpC unfoldase and especially lay a foundation toward the complete understanding of the structural dynamics of the general type II AAA(+) hexamers.
ダウンロード / ファイル: emd_5609.map.gz / 形式: CCP4 / 大きさ: 12.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
Reconstruction of MecA-ClpC(E280A,E618A) complex with ATP state
ボクセルのサイズ
X=Y=Z: 1.5 Å
密度
表面レベル
登録者による: 1.5 / ムービー #1: 1.5
最小 - 最大
-4.93566799 - 7.70951939
平均 (標準偏差)
0.00010409 (±0.99860597)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
-74
-74
-74
サイズ
150
150
150
Spacing
150
150
150
セル
A=B=C: 225.0 Å α=β=γ: 90.0 °
CCP4マップ ヘッダ情報:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.5
1.5
1.5
M x/y/z
150
150
150
origin x/y/z
0.000
0.000
0.000
length x/y/z
225.000
225.000
225.000
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-132
-122
-147
NX/NY/NZ
250
274
261
MAP C/R/S
1
2
3
start NC/NR/NS
-74
-74
-74
NC/NR/NS
150
150
150
D min/max/mean
-4.936
7.710
0.000
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添付データ
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試料の構成要素
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全体 : MecA-ClpC (E280A,E618A) with ATP
全体
名称: MecA-ClpC (E280A,E618A) with ATP
要素
試料: MecA-ClpC (E280A,E618A) with ATP
タンパク質・ペプチド: MecA
タンパク質・ペプチド: ClpC
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超分子 #1000: MecA-ClpC (E280A,E618A) with ATP
超分子
名称: MecA-ClpC (E280A,E618A) with ATP / タイプ: sample / ID: 1000 詳細: Mutant was generated by introducing double Walker B mutations: E280A and E618A. The mutant ClpC can bind ATP but not be able to hydrolyze ATP. 集合状態: Hexamer of ClpC with 6 bound MecA / Number unique components: 2
Protocol: Initial local fitting was done using Chimera and then MDFF was used for flexible fitting. ref: Trabuco, L.G., Villa, E., Mitra, K., Frank, J. and Schulten, K. (2008) Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure, 16, 673-683
精密化
空間: REAL / プロトコル: FLEXIBLE FIT / 当てはまり具合の基準: Cross-correlation
得られたモデル
PDB-3j3u: Structural dynamics of the MecA-ClpC complex revealed by cryo-EM