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- PDB-8k0g: Cryo-EM structure of human 26S RP (Ed state) bound to K11/K48-bra... -

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登録情報
データベース: PDB / ID: 8k0g
タイトルCryo-EM structure of human 26S RP (Ed state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub.
要素
  • (26S protease regulatory subunit ...) x 6
  • (26S proteasome non-ATPase regulatory subunit ...) x 11
  • (Proteasome subunit alpha type- ...) x 7
  • 26S proteasome complex subunit DSS1
  • Polyubiquitin-B
  • Protein SIC1
キーワードCYTOSOLIC PROTEIN / protein degradation / macromolecular complex / ubiquitin-proteasome system
機能・相同性
機能・相同性情報


SCF ubiquitin ligase complex binding / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / positive regulation of inclusion body assembly / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; オメガペプチターゼ / integrator complex / proteasome accessory complex ...SCF ubiquitin ligase complex binding / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / positive regulation of inclusion body assembly / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; オメガペプチターゼ / integrator complex / proteasome accessory complex / meiosis I / cyclin-dependent protein serine/threonine kinase inhibitor activity / purine ribonucleoside triphosphate binding / proteasome regulatory particle / cytosolic proteasome complex / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / hypothalamus gonadotrophin-releasing hormone neuron development / protein K63-linked deubiquitination / female meiosis I / negative regulation of programmed cell death / metal-dependent deubiquitinase activity / positive regulation of protein monoubiquitination / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / fat pad development / mitochondrion transport along microtubule / proteasome core complex / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Somitogenesis / Resolution of D-loop Structures through Holliday Junction Intermediates / K63-linked deubiquitinase activity / negative regulation of macroautophagy / female gonad development / Impaired BRCA2 binding to RAD51 / seminiferous tubule development / proteasome binding / transcription factor binding / regulation of protein catabolic process / myofibril / male meiosis I / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / blastocyst development / polyubiquitin modification-dependent protein binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / protein deubiquitination / immune system process / NF-kappaB binding / endopeptidase activator activity / proteasome assembly / mRNA export from nucleus / proteasome core complex, alpha-subunit complex / energy homeostasis / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / regulation of neuron apoptotic process / neuron projection morphogenesis / enzyme regulator activity / regulation of proteasomal protein catabolic process / ERAD pathway / Maturation of protein E / Maturation of protein E / inclusion body / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex
類似検索 - 分子機能
: / Ubiquitin interaction motif / : / 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 / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / 26S proteasome regulatory subunit RPN5 C-terminal domain ...: / Ubiquitin interaction motif / : / 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 / 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 / DSS1/SEM1 / : / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN11 C-terminal domain / DSS1_SEM1 / 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 / Proteasome/cyclosome repeat / : / 26S proteasome regulatory subunit 7, OB domain / Ubiquitin-interacting motif. / Proteasome/cyclosome repeat / : / : / : / 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 / von Willebrand factor type A domain / : / PCI/PINT associated module / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / HEAT repeats / Proteasome subunit alpha 1 / 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 subunit alpha5 / Proteasome subunit alpha6 / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / von Willebrand factor, type A / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / MPN domain / MPN domain profile. / ATPase, AAA-type, conserved site / AAA-protein family signature. / Nucleophile aminohydrolases, N-terminal / von Willebrand factor A-like domain superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / Proteasome subunit alpha type-7 / 26S proteasome non-ATPase regulatory subunit 3 / Polyubiquitin-B / 26S proteasome regulatory subunit 6A / Proteasome subunit alpha type-1 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / Proteasome subunit alpha type-7 / 26S proteasome non-ATPase regulatory subunit 3 / Polyubiquitin-B / 26S proteasome regulatory subunit 6A / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / 26S proteasome regulatory subunit 7 / Protein SIC1 / 26S proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome complex subunit SEM1 / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B / 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 13
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Saccharomyces cerevisiae (パン酵母)
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: 3.8 Å
データ登録者Hsu, S.T.D. / Draczkowski, P. / Wang, Y.S.
資金援助 台湾, 4件
組織認可番号国
Academia Sinica (Taiwan)AS-CDA-109- L08 台湾
Ministry of Science and Technology (MoST, Taiwan)MOST 109-3114-Y-001-001 台湾
Ministry of Science and Technology (MoST, Taiwan)MOST 110-2113-M-001- 050-MY3 台湾
Ministry of Science and Technology (MoST, Taiwan)110-2311-B-001-013-MY3 台湾
引用ジャーナル: Nat Commun / 年: 2025
タイトル: Structural basis of K11/K48-branched ubiquitin chain recognition by the human 26S proteasome.
著者: Piotr Draczkowski / Szu-Ni Chen / Ting Chen / Yong-Sheng Wang / Hsin-An Shih / Jessica Y C Huang / Ming-Chieh Tsai / Shu-Yu Lin / Steven Lin / Rosa Viner / Yuan-Chih Chang / Kuen-Phon Wu / Shang-Te Danny Hsu /
要旨: Beyond the canonical K48-linked homotypic polyubiquitination for proteasome-targeted proteolysis, K11/K48-branched ubiquitin (Ub) chains are involved in fast-tracking protein turnover during cell ...Beyond the canonical K48-linked homotypic polyubiquitination for proteasome-targeted proteolysis, K11/K48-branched ubiquitin (Ub) chains are involved in fast-tracking protein turnover during cell cycle progression and proteotoxic stress. Here, we report cryo-EM structures of human 26S proteasome in a complex with a K11/K48-branched Ub chain. The structures revealed a multivalent substrate recognition mechanism involving a hitherto unknown K11-linked Ub binding site at the groove formed by RPN2 and RPN10 in addition to the canonical K48-linkage binding site formed by RPN10 and RPT4/5 coiled-coil. Additionally, RPN2 recognizes an alternating K11-K48-linkage through a conserved motif similar to the K48-specific T1 binding site of RPN1. The insights gleaned from these structures explain the molecular mechanism underlying the recognition of the K11/K48-branched Ub as a priority signal in the ubiquitin-mediated proteasomal degradation.
履歴
登録2023年7月9日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02025年1月22日Provider: repository / タイプ: Initial release
改定 1.12025年11月5日Group: Data collection / Database references / カテゴリ: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: 26S protease regulatory subunit 7
B: 26S protease regulatory subunit 4
D: 26S protease regulatory subunit 6B
F: 26S protease regulatory subunit 6A
C: 26S protease regulatory subunit 8
G: Proteasome subunit alpha type-6
H: Proteasome subunit alpha type-2
I: Proteasome subunit alpha type-4
J: Proteasome subunit alpha type-7
K: Proteasome subunit alpha type-5
L: Proteasome subunit alpha type-1
M: Proteasome subunit alpha type-3
V: 26S proteasome non-ATPase regulatory subunit 3
W: 26S proteasome non-ATPase regulatory subunit 12
X: 26S proteasome non-ATPase regulatory subunit 11
Y: 26S proteasome non-ATPase regulatory subunit 6
d: 26S proteasome non-ATPase regulatory subunit 8
e: 26S proteasome complex subunit DSS1
f: 26S proteasome non-ATPase regulatory subunit 2
y: Protein SIC1
E: 26S protease regulatory subunit 10B
U: 26S proteasome non-ATPase regulatory subunit 1
Z: 26S proteasome non-ATPase regulatory subunit 7
a: 26S proteasome non-ATPase regulatory subunit 13
b: 26S proteasome non-ATPase regulatory subunit 4
c: 26S proteasome non-ATPase regulatory subunit 14
u: Polyubiquitin-B
v: Polyubiquitin-B
w: Polyubiquitin-B
x: Polyubiquitin-B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,142,30239
ポリマ－1,139,82930
非ポリマー2,4739
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: 電子顕微鏡法, negative stain TEM, mass spectrometry, native gel electrophoresis, cross-linking
タイプ名称対称操作数
identity operation1_5551

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要素

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26S protease regulatory subunit ... , 6種, 6分子 ABDFCE

#1: タンパク質 26S protease regulatory subunit 7 / 26S proteasome AAA-ATPase subunit RPT1 / Proteasome 26S subunit ATPase 2 / Protein MSS1


分子量: 48700.805 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMC2, MSS1 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P35998
#2: タンパク質 26S protease regulatory subunit 4 / P26s4 / 26S proteasome AAA-ATPase subunit RPT2 / Proteasome 26S subunit ATPase 1


分子量: 49260.504 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMC1 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P62191
#3: タンパク質 26S protease regulatory subunit 6B / 26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ...26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ATPase 4 / Tat-binding protein 7 / TBP-7


分子量: 47426.141 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMC4, MIP224, TBP7 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P43686
#4: タンパク質 26S protease regulatory subunit 6A / 26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / ...26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / Tat-binding protein 1 / TBP-1


分子量: 49266.457 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMC3, TBP1 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P17980
#5: タンパク質 26S protease regulatory subunit 8 / 26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / ...26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / Thyroid hormone receptor-interacting protein 1 / TRIP1 / p45/SUG


分子量: 45694.047 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMC5, SUG1 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P62195
#21: タンパク質 26S protease regulatory subunit 10B / 26S proteasome AAA-ATPase subunit RPT4 / Proteasome 26S subunit ATPase 6 / Proteasome subunit p42


分子量: 44241.008 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMC6, SUG2 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P62333

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Proteasome subunit alpha type- ... , 7種, 7分子 GHIJKLM

#6: タンパク質 Proteasome subunit alpha type-6 / 27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota ...27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


分子量: 27432.459 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMA6, PROS27 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P60900, proteasome endopeptidase complex
#7: タンパク質 Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


分子量: 25927.535 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMA2, HC3, PSC3 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P25787, proteasome endopeptidase complex
#8: タンパク質 Proteasome subunit alpha type-4 / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / ...Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


分子量: 29525.842 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMA4, HC9, PSC9 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P25789, proteasome endopeptidase complex
#9: タンパク質 Proteasome subunit alpha type-7 / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


分子量: 27929.891 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMA7, HSPC / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O14818, proteasome endopeptidase complex
#10: タンパク質 Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


分子量: 26435.977 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMA5 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P28066, proteasome endopeptidase complex
#11: タンパク質 Proteasome subunit alpha type-1 / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex ...30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


分子量: 29595.627 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMA1, HC2, NU, PROS30, PSC2 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P25786, proteasome endopeptidase complex
#12: タンパク質 Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


分子量: 28469.252 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMA3, HC8, PSC8 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P25788

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26S proteasome non-ATPase regulatory subunit ... , 11種, 11分子 VWXYdfUZabc

#13: タンパク質 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit RPN3 / 26S proteasome regulatory subunit S3 / Proteasome subunit p58


分子量: 61066.500 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD3 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O43242
#14: タンパク質 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit p55


分子量: 52979.359 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD12 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O00232
#15: タンパク質 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit S9 / 26S proteasome ...26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit S9 / 26S proteasome regulatory subunit p44.5


分子量: 47526.688 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD11 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O00231
#16: タンパク質 26S proteasome non-ATPase regulatory subunit 6 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit S10 / Breast cancer- ...26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit S10 / Breast cancer-associated protein SGA-113M / Phosphonoformate immuno-associated protein 4 / Proteasome regulatory particle subunit p44S10 / p42A


分子量: 45592.285 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD6, KIAA0107, PFAAP4 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q15008
#17: タンパク質 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit S14 / p31


分子量: 39667.871 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD8 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P48556
#19: タンパク質 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit S2 / 26S proteasome ...26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit S2 / 26S proteasome subunit p97 / Protein 55.11 / Tumor necrosis factor type 1 receptor-associated protein 2


分子量: 100313.625 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD2, TRAP2 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q13200
#22: タンパク質 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome subunit p112


分子量: 105958.234 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD1 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q99460
#23: タンパク質 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit S12 / Mov34 protein ...26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit S12 / Mov34 protein homolog / Proteasome subunit p40


分子量: 37086.441 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD7, MOV34L / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P51665
#24: タンパク質 26S proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit S11 / 26S proteasome ...26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit S11 / 26S proteasome regulatory subunit p40.5


分子量: 42995.359 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD13 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9UNM6
#25: タンパク質 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory ...26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory factor 1 / ASF / Multiubiquitin chain-binding protein


分子量: 40781.590 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD4, MCB1 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P55036
#26: タンパク質 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome regulatory subunit RPN11 / 26S proteasome-associated PAD1 homolog 1


分子量: 34620.023 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMD14, POH1 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト)
参照: UniProt: O00487, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; オメガペプチターゼ

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タンパク質 , 3種, 6分子 eyuvwx

#18: タンパク質 26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot ...Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot malformation type 1 protein


分子量: 8284.611 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SHFM1, DSS1, SHFDG1 / 細胞株 (発現宿主): HEK293 / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P60896
#20: タンパク質 Protein SIC1 / CDK inhibitor p40


分子量: 7249.966 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: SIC1, SDB25, YLR079W, L9449.8 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): Codon Plus RIL / 参照: UniProt: P38634
#27: タンパク質
Polyubiquitin-B


分子量: 8950.154 Da / 分子数: 4 / Mutation: K63R / 由来タイプ: 組換発現
詳細: GSGGS linker sequence remaining at C-terminus after TEV cleavage
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBB / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): Codon Plus RIL / 参照: UniProt: P0CG47

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非ポリマー , 3種, 9分子

#28: 化合物 ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


分子量: 507.181 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C10H16N5O13P3 / タイプ: SUBJECT OF INVESTIGATION / コメント: ATP, エネルギー貯蔵分子*YM
#29: 化合物
ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Mg / タイプ: SUBJECT OF INVESTIGATION
#30: 化合物 ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


分子量: 427.201 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: ADP, エネルギー貯蔵分子*YM

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

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実験情報

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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

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試料調製

構成要素
ID名称タイプ詳細Entity IDParent-ID由来
1Human 26S proteasomeCOMPLEXImages of double-capped (RP-CP-RP) 26S proteasome particles were split in half. After combining with subset of single-capped (RP-CP) complexes the signal in particle images was partially subtracted leaving only the signal of 19S RP together with alpha subunits of the 20S CP proteasomal subcomplex.#1-#270RECOMBINANT
219S regulatory particle (RP) of human 26S proteasomeCOMPLEX#1-#5, #13-#19, #21-#261RECOMBINANT
3AAA+-ATPase of 19S regulatory particle (RP) of human 26S proteasomeCOMPLEX#1-#5, #212RECOMBINANT
4alpha subunits of the 20S core particle (CP) of human 26S proteasomeCOMPLEX#6-#121RECOMBINANT
5Ubiquitinated substrateCOMPLEXSic1_PY conjugated with K11/K48-branched ubiquitin chain.#20, #271RECOMBINANT
6K11/K48-branched ubiquitin (Ub) chain composed of four Ub.COMPLEX#275RECOMBINANT
7Sic1_PY substrate polypeptideCOMPLEX#205RECOMBINANT
分子量値: 2.5 MDa / 実験値: NO
由来(天然)
IDEntity assembly-ID生物種Ncbi tax-ID
21Homo sapiens (ヒト)9606
42Homo sapiens (ヒト)9606
54Homo sapiens (ヒト)9606
76Homo sapiens (ヒト)9606
87Saccharomyces cerevisiae (パン酵母)4932
由来(組換発現)
IDEntity assembly-ID生物種Ncbi tax-ID細胞
21Homo sapiens (ヒト)9606HEK-293
32Homo sapiens (ヒト)9606HEK-293
55Escherichia coli BL21(DE3) (大腸菌)469008
76Homo sapiens (ヒト)9606HEK-293
87Homo sapiens (ヒト)9606HEK-293
緩衝液pH: 7.6
緩衝液成分
ID濃度名称式Buffer-ID
120 mMHEPESC8H18N2O4S1
240 mMsodium chlorideNaCl1
35 mMmagnesium chlorideMgCl21
42 mM2-MercaptoethanolC2H6OS1
50.5 mM1,10-PhenanthrolineC12H8N21
62 mMadenosine triphosphateC10H16N5O13P31
試料濃度: 1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
詳細: The complex was additionally supplemented with an excess of preformed and SEC-purified RPN13:UCHL5 complex.
試料支持詳細: 20 mA / グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3
急速凍結装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277.15 K / 詳細: incubation time= 3 s blotting time= 2.5 s

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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 / 倍率（公称値）: 70000 X / 最大 デフォーカス（公称値）: 1800 nm / 最小 デフォーカス（公称値）: 1200 nm / アライメント法: COMA FREE
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影平均露光時間: 1.8 sec. / 電子線照射量: 49 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 3 / 実像数: 15242
電子光学装置エネルギーフィルタースリット幅: 20 eV

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解析

EMソフトウェア
ID名称バージョンカテゴリ
1Topaz粒子像選択
2EPU画像取得
4CTFFIND4.1CTF補正
7UCSF ChimeraX1.3モデルフィッティング
9ISOLDE1.3モデル精密化
10Coot0.9.4.1 ELモデル精密化
11PHENIX1.19.2モデル精密化
12RELION3.1初期オイラー角割当
13cryoSPARC3.1最終オイラー角割当
14RELION3.1分類
15cryoSPARC3.1３次元再構成
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
粒子像の選択選択した粒子像数: 2695911
対称性点対称性: C1 (非対称)
3次元再構成解像度: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 84476 / アルゴリズム: FOURIER SPACE
詳細: Performed in cryoSPARC using Non-uniform Refinement job type. Some parts of the map were then improved by using focused local refinement.
クラス平均像の数: 2 / 対称性のタイプ: POINT
原子モデル構築B value: 107.54 / プロトコル: OTHER / 空間: REAL / Target criteria: 0.83
原子モデル構築PDB-ID: 6MSK

6msk


Accession code: 6MSK / Source name: PDB / タイプ: experimental model
精密化交差検証法: NONE
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
原子変位パラメータBiso mean: 107.44 Å2
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.007969855
ELECTRON MICROSCOPYf_angle_d0.882194619
ELECTRON MICROSCOPYf_chiral_restr0.051911015
ELECTRON MICROSCOPYf_plane_restr0.006412337
ELECTRON MICROSCOPYf_dihedral_angle_d14.513125341

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万見について

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お知らせ

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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

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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

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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

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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

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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。

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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

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