EMDB-6579: Cryo-EM map of yeast 26S proteasome in M2 state with RP mask deri...

基本情報

• 登録情報: データベース: EMDB / ID: EMD-6579
• タイトル: Cryo-EM map of yeast 26S proteasome in M2 state with RP mask derived from Arctica dataset
• マップデータ: Reconstruction of single particle

試料

• 試料: RP of yeast 26S proteasome in M2 state
• タンパク質・ペプチド: 19S RP of proteasome

機能・相同性

分子機能:

SAGA complex localization to transcription regulatory region / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / nonfunctional rRNA decay / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / protein-containing complex localization / mitochondrial fission / proteasome regulatory particle, base subcomplex / K48-linked polyubiquitin modification-dependent protein binding / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / peptide catabolic process / proteasome binding / regulation of protein catabolic process / protein deubiquitination / proteasome storage granule / polyubiquitin modification-dependent protein binding / endopeptidase activator activity / proteasome assembly / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / enzyme regulator activity / mRNA export from nucleus / : / protein folding chaperone / Neutrophil degranulation / proteasome complex / ubiquitin binding / proteasomal protein catabolic process / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / positive regulation of protein catabolic process / metallopeptidase activity / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / regulation of cell cycle / クロマチンリモデリング / protein domain specific binding / mRNA binding / ubiquitin protein ligase binding / structural molecule activity / endoplasmic reticulum membrane / 小胞体 / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / ミトコンドリア / ATP binding / identical protein binding / metal ion binding / 細胞核 / 細胞質基質 / 細胞質

ドメイン・相同性:

Rpn9, C-terminal helix / Rpn9 C-terminal helix / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / DSS1/SEM1 / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S proteasome subunit RPN2, N-terminal domain / DSS1_SEM1 / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S Proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S Proteasome non-ATPase regulatory subunit 7/8 / : / 26S proteasome regulatory subunit 7, OB domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / PCI/PINT associated module / von Willebrand factor type A domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / HEAT repeats / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / VWFA domain profile. / Proteasome subunit / Proteasome, subunit alpha/beta / von Willebrand factor, type A / AAA ATPase, AAA+ lid domain / AAA+ lid domain / TPR repeat region circular profile. / ATPase, AAA-type, conserved site / AAA-protein family signature. / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / TPR repeat profile. / MPN domain / MPN domain profile. / Nucleophile aminohydrolases, N-terminal / von Willebrand factor A-like domain superfamily / Tetratricopeptide repeat / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities

構成要素:

26S proteasome regulatory subunit RPN13 / 26S proteasome complex subunit SEM1 / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 6B homolog / 26S proteasome regulatory subunit 7 homolog / Proteasome subunit beta type-1 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit RPN3 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / 26S proteasome regulatory subunit 4 homolog / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome subunit RPT4 / 26S proteasome regulatory subunit 8 homolog / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit RPN6

• 生物種: Saccharomyces cerevisiae (パン酵母)
• 手法: 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 8.7 Å
• データ登録者: Luan B / Huang XL / Wu JP / Shi YG / Wang F
• 引用: ジャーナル: Proc Natl Acad Sci U S A / 年: 2016; タイトル: Structure of an endogenous yeast 26S proteasome reveals two major conformational states.; 著者: Bai Luan / Xiuliang Huang / Jianping Wu / Ziqing Mei / Yiwei Wang / Xiaobin Xue / Chuangye Yan / Jiawei Wang / Daniel J Finley / Yigong Shi / Feng Wang / ; 要旨: The eukaryotic proteasome mediates degradation of polyubiquitinated proteins. Here we report the single-particle cryoelectron microscopy (cryo-EM) structures of the endogenous 26S proteasome from Saccharomyces cerevisiae at 4.6- to 6.3-Å resolution. The fine features of the cryo-EM maps allow modeling of 18 subunits in the regulatory particle and 28 in the core particle. The proteasome exhibits two distinct conformational states, designated M1 and M2, which correspond to those reported previously for the proteasome purified in the presence of ATP-γS and ATP, respectively. These conformations also correspond to those of the proteasome in the presence and absence of exogenous substrate. Structure-guided biochemical analysis reveals enhanced deubiquitylating enzyme activity of Rpn11 upon assembly of the lid. Our structures serve as a molecular basis for mechanistic understanding of proteasome function.

履歴

登録	2016年1月7日	-
ヘッダ(付随情報) 公開	2016年3月30日	-
マップ公開	2016年5月11日	-
更新	2016年6月1日	-
現状	2016年6月1日	処理サイト: PDBj / 状態: 公開

マップ

• ファイル: ダウンロード / ファイル: emd_6579.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 single particle
• ボクセルのサイズ: X=Y=Z: 2.54 Å

密度

表面レベル	登録者による: 0.146 / ムービー #1: 0.13
最小 - 最大	-0.11261199 - 0.29786244
平均 (標準偏差)	0.0004957 (±0.01359515)

• 対称性: 空間群: 1

詳細

EMDB XML:

マップ形状	Axis order X Y Z Origin 0 0 0 サイズ 256 256 256 Spacing 256 256 256
セル	A=B=C: 650.24 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	2.54	2.54	2.54
M x/y/z	256	256	256
origin x/y/z	0.000	0.000	0.000
length x/y/z	650.240	650.240	650.240
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	256	256	256
D min/max/mean	-0.113	0.298	0.000

添付データ

試料の構成要素

全体 : RP of yeast 26S proteasome in M2 state

• 全体: 名称: RP of yeast 26S proteasome in M2 state

要素

• 試料: RP of yeast 26S proteasome in M2 state
• タンパク質・ペプチド: 19S RP of proteasome

超分子 #1000: RP of yeast 26S proteasome in M2 state

• 超分子: 名称: RP of yeast 26S proteasome in M2 state / タイプ: sample / ID: 1000 / 詳細: The sample was monodisperse / Number unique components: 1
• 分子量: 実験値: 2.5 MDa / 理論値: 2.5 MDa

分子 #1: 19S RP of proteasome

• 分子: 名称: 19S RP of proteasome / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 組換発現: No / データベース: NCBI
• 由来(天然): 生物種: Saccharomyces cerevisiae (パン酵母) / 別称: Yeast / 細胞中の位置: Cytoplasma
• 分子量: 実験値: 2.5 MDa / 理論値: 2.5 MDa

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: 15 mg/mL
• 緩衝液: pH: 7.5 / 詳細: 50mM Tris7.5, 100mM NaCl, 5mM MgCl2, 2mM ATP
• グリッド: 詳細: Quantifoil Cu R2.0/2.0 200 mesh
• 凍結: 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: FEI VITROBOT MARK IV

電子顕微鏡法

• 顕微鏡: OTHER
• 電子線: 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN
• 電子光学系: 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 最大 デフォーカス（公称値）: 0.0032 µm / 最小 デフォーカス（公称値）: 0.0016 µm / 倍率（公称値）: 78000
• 試料ステージ: 試料ホルダーモデル: OTHER
• 温度: 平均: 100 K
• 日付: 2015年11月2日
• 撮影: カテゴリ: CCD; フィルム・検出器のモデル: FEI FALCON II (4k x 4k); 実像数: 6570 ; 詳細: Every image is the average of 21 frames recorded by the direct electron detector

画像解析

• CTF補正: 詳細: Each micrographs
• 最終 再構成: 解像度のタイプ: BY AUTHOR / 解像度: 8.7 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: 16063
• 詳細: The particles were selected in RELION and manually checked. 3D classification and refinement were performed in RELION.