[日本語] English
万見
- PDB-9iwr: 26S proteasome trimer -

+
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: PDB / ID: 9iwr
タイトル26S proteasome trimer
要素
  • (26S protease regulatory subunit ...) x 5
  • (26S proteasome regulatory subunit ...) x 11
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • 26S protease subunit RPT4
  • 26S proteasome complex subunit SEM1
  • Probable proteasome subunit alpha type-7
  • Ubiquitin carboxyl-terminal hydrolase RPN11
キーワードHYDROLASE / proteasome / trimer / complex / PSG / paracrystalline
機能・相同性
機能・相同性情報


SAGA complex localization to transcription regulatory region / : / proteasome regulatory particle assembly / proteasome storage granule assembly / transcription export complex 2 / peroxisome fission / maintenance of DNA trinucleotide repeats / protein deneddylation / filamentous growth / COP9 signalosome ...SAGA complex localization to transcription regulatory region / : / proteasome regulatory particle assembly / proteasome storage granule assembly / transcription export complex 2 / peroxisome fission / maintenance of DNA trinucleotide repeats / protein deneddylation / filamentous growth / COP9 signalosome / mitochondrial fission / proteasome regulatory particle / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / ER-Phagosome pathway / Antigen processing: Ub, ATP-independent proteasomal degradation / protein-containing complex localization / proteasome core complex assembly / Proteasome assembly / K48-linked polyubiquitin modification-dependent protein binding / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / nuclear outer membrane-endoplasmic reticulum membrane network / nonfunctional rRNA decay / metal-dependent deubiquitinase activity / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / peptide catabolic process / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome binding / regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / proteasome storage granule / proteasomal ubiquitin-independent protein catabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / protein deubiquitination / Ub-specific processing proteases / polyubiquitin modification-dependent protein binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / endopeptidase activator activity / threonine-type endopeptidase activity / proteasome assembly / mRNA export from nucleus / proteasome core complex, alpha-subunit complex / enzyme regulator activity / ERAD pathway / Neutrophil degranulation / protein folding chaperone / proteasome complex / nucleotide-excision repair / ubiquitin binding / positive regulation of transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / metallopeptidase activity / positive regulation of protein catabolic process / peroxisome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / endopeptidase activity / molecular adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / cysteine-type deubiquitinase activity / ubiquitinyl hydrolase 1 / regulation of cell cycle / chromatin remodeling / protein domain specific binding / mRNA binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
類似検索 - 分子機能
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 ...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 / PSMD3-like, N-terminal TPR repeats / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / 26S proteasome regulatory subunit RPN5 C-terminal domain / PSD13 N-terminal repeats / 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 non-ATPase regulatory subunit 13 / : / 26S proteasome subunit RPN2, N-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / Proteasome subunit Rpn10 / 26S Proteasome non-ATPase regulatory subunit 7/8 / 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 RPN11 C-terminal domain / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / Proteasome/cyclosome repeat / : / 26S proteasome regulatory subunit 7, OB domain / Proteasome/cyclosome repeat / von Willebrand factor type A domain / : / : / : / PSMD12/CSN4, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome subunit RPN7 / : / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / PCI/PINT associated module / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / HEAT repeats / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / 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 alpha5 / Proteasome subunit alpha6 / 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 B-type subunit / VWFA domain profile. / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / TPR repeat region circular profile. / von Willebrand factor, type A / TPR repeat profile. / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / AAA ATPase, AAA+ lid domain
類似検索 - ドメイン・相同性
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 ...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 C-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
類似検索 - 構成要素
生物種Saccharomyces cerevisiae S288C (パン酵母)
手法電子顕微鏡法 / サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 9.1 Å
データ登録者Qu, L. / Tang, X. / Baumeister, W.
資金援助 ドイツ, 2件
組織認可番号国
Max Planck Society ドイツ
Jung foundation ドイツ
引用ジャーナル: Cell / 年: 2026
タイトル: Metabolically regulated proteasome supramolecular organization in situ.
著者: Xiaomeng Tang / Lu Qu / Florian Wilfling / Florian Beck / Oliver P Ernst / Brenda A Schulman / Wolfgang Baumeister / Cordula Enenkel /
要旨: Many proteins localize in membraneless organelles. However, understanding the steps along membraneless organelle formation-and the structural impact on granule constituents-has been hindered by ...Many proteins localize in membraneless organelles. However, understanding the steps along membraneless organelle formation-and the structural impact on granule constituents-has been hindered by limited resolution of intracellular data. We address these challenges through in situ cryo-electron tomography (cryo-ET) along with formation of yeast proteasome storage granules (PSGs). During the transition from proliferation to quiescence, doubly capped 26S proteasomes arrested in an inactive state arrange into ∼7.5 MDa trimeric units, dispersed in the nucleoplasm and congregated along the nuclear envelope near the nuclear pore. 9-Å-resolution cryo-ET structures reveal that cytoplasmic PSGs formed in various energy-limiting conditions are paracrystalline arrays of bundled fibers, assembled from stacking of proteasome trimers. The paracrystalline arrangement maintains a pool of fully assembled inactive 26S proteasomes that are released in energy-rich conditions. Overall, our data reveal structural steps along the assembly of an intracellular membraneless organelle in situ and quinary structure formation controlling a major eukaryotic regulatory machine.
履歴
登録2024年7月25日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02026年1月28日Provider: repository / タイプ: Initial release
改定 1.02026年1月28日Data content type: EM metadata / Data content type: EM metadata / Provider: repository / タイプ: Initial release
改定 1.02026年1月28日Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / タイプ: Initial release
改定 1.02026年1月28日Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / タイプ: Initial release
改定 1.02026年1月28日Data content type: Image / Data content type: Image / Provider: repository / タイプ: Initial release
改定 1.02026年1月28日Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / タイプ: Initial release
改定 1.02026年1月28日Data content type: Primary map / Data content type: Primary map / Provider: repository / タイプ: Initial release
改定 1.12026年3月4日Group: Data collection / Database references / Structure summary
カテゴリ: audit_author / citation ...audit_author / citation / citation_author / em_admin
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
改定 1.12026年3月4日Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / カテゴリ: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

-
集合体

登録構造単位
1: Proteasome subunit beta type-1
2: Proteasome subunit beta type-2
3: Proteasome subunit beta type-3
4: Proteasome subunit beta type-4
5: Proteasome subunit beta type-5
6: Proteasome subunit beta type-6
7: Proteasome subunit beta type-7
A: Proteasome subunit alpha type-1
B: Proteasome subunit alpha type-2
C: Proteasome subunit alpha type-3
D: Proteasome subunit alpha type-4
E: Proteasome subunit alpha type-5
F: Proteasome subunit alpha type-6
G: Probable proteasome subunit alpha type-7
H: 26S protease regulatory subunit 7 homolog
I: 26S protease regulatory subunit 4 homolog
J: 26S protease regulatory subunit 8 homolog
K: 26S protease regulatory subunit 6B homolog
L: 26S protease subunit RPT4
M: 26S protease regulatory subunit 6A
N: 26S proteasome regulatory subunit RPN2
O: 26S proteasome regulatory subunit RPN9
P: 26S proteasome regulatory subunit RPN5
Q: 26S proteasome regulatory subunit RPN6
R: 26S proteasome regulatory subunit RPN7
S: 26S proteasome regulatory subunit RPN3
T: 26S proteasome regulatory subunit RPN12
U: 26S proteasome regulatory subunit RPN8
V: Ubiquitin carboxyl-terminal hydrolase RPN11
W: 26S proteasome regulatory subunit RPN10
X: 26S proteasome regulatory subunit RPN13
Y: 26S proteasome complex subunit SEM1
Z: 26S proteasome regulatory subunit RPN1
a: Proteasome subunit alpha type-1
b: Proteasome subunit alpha type-2
c: Proteasome subunit alpha type-3
d: Proteasome subunit alpha type-4
e: Proteasome subunit alpha type-5
f: Proteasome subunit alpha type-6
g: Probable proteasome subunit alpha type-7
h: Proteasome subunit beta type-1
i: Proteasome subunit beta type-2
j: Proteasome subunit beta type-3
k: Proteasome subunit beta type-4
l: Proteasome subunit beta type-5
m: Proteasome subunit beta type-6
n: Proteasome subunit beta type-7


分子量 (理論値)分子数
合計 (水以外)1,692,66047
ポリマ－1,692,66047
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: 電子顕微鏡法, not applicable
タイプ名称対称操作数
identity operation1_555x,y,z1
モデル数3

-
要素

-
Proteasome subunit beta type- ... , 7種, 14分子 1h2i3j4k5l6m7n

#1: タンパク質 Proteasome subunit beta type-1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component ...Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


分子量: 23573.604 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: PRE3, YJL001W, J1407 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P38624, proteasome endopeptidase complex
#2: タンパク質 Proteasome subunit beta type-2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component ...Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component PUP1 / Proteinase YSCE subunit PUP1


分子量: 28299.889 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: PUP1, YOR157C / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P25043, proteasome endopeptidase complex
#3: タンパク質 Proteasome subunit beta type-3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


分子量: 22627.842 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: PUP3, YER094C / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P25451, proteasome endopeptidase complex
#4: タンパク質 Proteasome subunit beta type-4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 ...Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 / Proteinase YSCE subunit 11


分子量: 22545.676 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: PRE1, YER012W / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P22141, proteasome endopeptidase complex
#5: タンパク質 Proteasome subunit beta type-5 / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component ...Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component PRE2 / Proteinase YSCE subunit PRE2


分子量: 31670.539 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: PRE2, DOA3, PRG1, YPR103W, P8283.10 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P30656, proteasome endopeptidase complex
#6: タンパク質 Proteasome subunit beta type-6 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


分子量: 26905.076 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: PRE7, PRS3, PTS1, YBL041W, YBL0407 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P23724, proteasome endopeptidase complex
#7: タンパク質 Proteasome subunit beta type-7 / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component ...Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component PRE4 / Proteinase YSCE subunit PRE4


分子量: 29471.289 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: PRE4, YFR050C / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P30657, proteasome endopeptidase complex

-
Proteasome subunit alpha type- ... , 6種, 12分子 AaBbCcDdEeFf

#8: タンパク質 Proteasome subunit alpha type-1 / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7- ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7-alpha / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


分子量: 28033.830 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: SCL1, PRC2, PRS2, YGL011C / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P21243, proteasome endopeptidase complex
#9: タンパク質 Proteasome subunit alpha type-2 / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / ...Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


分子量: 27191.828 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: PRE8, PRS4, YML092C / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P23639, proteasome endopeptidase complex
#10: タンパク質 Proteasome subunit alpha type-3 / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 ...Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 / Proteinase YSCE subunit 13


分子量: 28748.230 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: PRE9, PRS5, YGR135W / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P23638, proteasome endopeptidase complex
#11: タンパク質 Proteasome subunit alpha type-4 / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component ...Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component PRE6 / Proteinase YSCE subunit PRE6


分子量: 28478.111 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: PRE6, YOL038W / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P40303, proteasome endopeptidase complex
#12: タンパク質 Proteasome subunit alpha type-5 / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component ...Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component PUP2 / Proteinase YSCE subunit PUP2


分子量: 28649.086 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: PUP2, DOA5, YGR253C, G9155 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P32379, proteasome endopeptidase complex
#13: タンパク質 Proteasome subunit alpha type-6 / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component ...Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component PRE5 / Proteinase YSCE subunit PRE5


分子量: 25634.000 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: PRE5, YMR314W, YM9924.06 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P40302, proteasome endopeptidase complex

-
タンパク質 , 4種, 5分子 GgLVY

#14: タンパク質 Probable proteasome subunit alpha type-7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / ...Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / Proteinase YSCE subunit 1


分子量: 31575.068 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: PRE10, PRC1, PRS1, YOR362C, O6650 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P21242, proteasome endopeptidase complex
#19: タンパク質 26S protease subunit RPT4 / 26S protease subunit SUG2 / Proteasomal cap subunit


分子量: 49480.137 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPT4, CRL13, PCS1, SUG2, YOR259C / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P53549
#29: タンパク質 Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit RPN11 / Protein MPR1


分子量: 34442.281 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPN11, MPR1, YFR004W / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P43588, ubiquitinyl hydrolase 1
#32: タンパク質 26S proteasome complex subunit SEM1


分子量: 10397.102 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: SEM1, DSH1, YDR363W-A / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: O94742

-
26S protease regulatory subunit ... , 5種, 5分子 HIJKM

#15: タンパク質 26S protease regulatory subunit 7 homolog / Protein CIM5 / Tat-binding homolog 3


分子量: 52054.891 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPT1, CIM5, YTA3, YKL145W / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P33299
#16: タンパク質 26S protease regulatory subunit 4 homolog / Tat-binding homolog 5


分子量: 48898.160 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPT2, YHS4, YTA5, YDL007W, D2920 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P40327
#17: タンパク質 26S protease regulatory subunit 8 homolog / Protein CIM3 / Protein SUG1 / Tat-binding protein TBY1


分子量: 45342.742 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPT6, CIM3, CRL3, SUG1, TBPY, TBY1, YGL048C / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: Q01939
#18: タンパク質 26S protease regulatory subunit 6B homolog / Protein YNT1 / Tat-binding homolog 2


分子量: 47953.676 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPT3, YNT1, YTA2, YDR394W, D9509.14 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P33298
#20: タンパク質 26S protease regulatory subunit 6A / Tat-binding protein homolog 1 / TBP-1


分子量: 48315.727 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPT5, YTA1, YOR117W, O3258, YOR3258W / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P33297

-
26S proteasome regulatory subunit ... , 11種, 11分子 NOPQRSTUWXZ

#21: タンパク質 26S proteasome regulatory subunit RPN2


分子量: 104351.883 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPN2, SEN3, YIL075C / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P32565
#22: タンパク質 26S proteasome regulatory subunit RPN9 / Proteasome non-ATPase subunit 7


分子量: 45839.348 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPN9, NAS7, YDR427W, D9461.14 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: Q04062
#23: タンパク質 26S proteasome regulatory subunit RPN5 / Proteasome non-ATPase subunit 5


分子量: 51840.352 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPN5, NAS5, YDL147W, D1572 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: Q12250
#24: タンパク質 26S proteasome regulatory subunit RPN6 / Proteasome non-ATPase subunit 4


分子量: 49839.812 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPN6, NAS4, YDL097C, D2381 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: Q12377
#25: タンパク質 26S proteasome regulatory subunit RPN7


分子量: 49016.367 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPN7, YPR108W, P8283.8 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: Q06103
#26: タンパク質 26S proteasome regulatory subunit RPN3


分子量: 60464.605 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPN3, SUN2, YER021W / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P40016
#27: タンパク質 26S proteasome regulatory subunit RPN12 / Nuclear integrity protein 1


分子量: 31952.119 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPN12, NIN1, YFR052W / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P32496
#28: タンパク質 26S proteasome regulatory subunit RPN8


分子量: 38365.508 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPN8, YOR261C, O5360 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: Q08723
#30: タンパク質 26S proteasome regulatory subunit RPN10


分子量: 29776.098 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPN10, MCB1, SUN1, YHR200W / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P38886
#31: タンパク質 26S proteasome regulatory subunit RPN13 / Proteasome non-ATPase subunit 13


分子量: 17919.002 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPN13, DAQ1, YLR421C / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: O13563
#33: タンパク質 26S proteasome regulatory subunit RPN1 / HMG-CoA reductase degradation protein 2 / Proteasome non-ATPase subunit 1


分子量: 109601.906 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPN1, HRD2, NAS1, RPD1, YHR027C / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P38764

-
詳細

Has protein modificationN

-
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: CELL / ３次元再構成法: サブトモグラム平均法

-
試料調製

構成要素名称: 26S proteasome trimer / タイプ: COMPLEX / Entity ID: all / 由来: NATURAL
由来(天然)生物種: Saccharomyces cerevisiae S288C (パン酵母)
緩衝液pH: 6.8 / 詳細: YPD buffer
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結凍結剤: ETHANE-PROPANE

-
電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
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 / 最大 デフォーカス（公称値）: 4000 nm / 最小 デフォーカス（公称値）: 3000 nm
撮影電子線照射量: 2.7 e/Å2 / Avg electron dose per subtomogram: 100 e/Å2
フィルム・検出器のモデル: FEI FALCON IV (4k x 4k)

-
解析

CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性点対称性: D3 (2回x3回 2面回転対称)
3次元再構成解像度: 9.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 1700 / 対称性のタイプ: POINT
EM volume selectionNum. of tomograms: 73 / Num. of volumes extracted: 1700

+
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