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- PDB-5l4g: The human 26S proteasome at 3.9 A -

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基本情報

登録情報
データベース: PDB / ID: 5l4g
タイトルThe human 26S proteasome at 3.9 A
要素
  • (26S protease regulatory subunit ...) x 6
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
キーワードHYDROLASE / proteostasis / AAA-ATPase
機能・相同性
機能・相同性情報


positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / proteasome accessory complex / purine ribonucleoside triphosphate binding / positive regulation of proteasomal protein catabolic process / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / negative regulation of programmed cell death ...positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / proteasome accessory complex / purine ribonucleoside triphosphate binding / positive regulation of proteasomal protein catabolic process / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / negative regulation of programmed cell death / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / : / Somitogenesis / myofibril / immune system process / transcription factor binding / blastocyst development / general transcription initiation factor binding / NF-kappaB binding / 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 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / ERAD pathway / inclusion body / sarcomere / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / proteolysis involved in protein catabolic process / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / negative regulation of inflammatory response to antigenic stimulus / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / lipopolysaccharide binding / Hh mutants are degraded by ERAD / Degradation of AXIN / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / G2/M Checkpoints / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / P-body / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / response to virus / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / response to organic cyclic compound / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / nuclear matrix / Regulation of PTEN stability and activity / Interleukin-1 signaling / cytoplasmic ribonucleoprotein granule / Orc1 removal from chromatin / osteoblast differentiation / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / positive regulation of NF-kappaB transcription factor activity / peptidase activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / protein-macromolecule adaptor activity
類似検索 - 分子機能
: / 26S proteasome regulatory subunit 7, OB domain / : / Proteasome subunit alpha 1 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 ...: / 26S proteasome regulatory subunit 7, OB domain / : / Proteasome subunit alpha 1 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / 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. / Proteasome subunit / Proteasome, subunit alpha/beta / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Nucleophile aminohydrolases, N-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Proteasome subunit alpha type-7 / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-1 / 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 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Proteasome subunit alpha type-7 / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-1 / 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 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B / Proteasome subunit beta type-7
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
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: 3.9 Å
データ登録者Schweitzer, A. / Aufderheide, A. / Rudack, T. / Beck, F.
引用ジャーナル: Proc Natl Acad Sci U S A / 年: 2016
タイトル: Structure of the human 26S proteasome at a resolution of 3.9 Å.
著者: Andreas Schweitzer / Antje Aufderheide / Till Rudack / Florian Beck / Günter Pfeifer / Jürgen M Plitzko / Eri Sakata / Klaus Schulten / Friedrich Förster / Wolfgang Baumeister /
要旨: Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades ...Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades polyubiquitylated proteins, and a regulatory particle (RP) containing the AAA-ATPase module. This module controls access to the proteolytic chamber inside the CP and is surrounded by non-ATPase subunits (Rpns) that recognize substrates and deubiquitylate them before unfolding and degradation. The architecture of the 26S holocomplex is highly conserved between yeast and humans. The structure of the human 26S holocomplex described here reveals previously unidentified features of the AAA-ATPase heterohexamer. One subunit, Rpt6, has ADP bound, whereas the other five have ATP in their binding pockets. Rpt6 is structurally distinct from the other five Rpt subunits, most notably in its pore loop region. For Rpns, the map reveals two main, previously undetected, features: the C terminus of Rpn3 protrudes into the mouth of the ATPase ring; and Rpn1 and Rpn2, the largest proteasome subunits, are linked by an extended connection. The structural features of the 26S proteasome observed in this study are likely to be important for coordinating the proteasomal subunits during substrate processing.
履歴
登録2016年5月25日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02016年9月7日Provider: repository / タイプ: Initial release
改定 1.12016年9月21日Group: Database references
改定 1.22017年8月2日Group: Data collection / Derived calculations
カテゴリ: em_image_scans / em_software ...em_image_scans / em_software / pdbx_struct_conn_angle / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _em_software.name
改定 1.32019年12月11日Group: Other / カテゴリ: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
改定 1.42024年5月8日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_high / _refine.ls_d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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構造の表示

ムービー
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  • マップデータ: EMDB-4002
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ムービービューア
構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
N: Proteasome subunit alpha type-6
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-4
Q: Proteasome subunit alpha type-7
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-1
T: Proteasome subunit alpha type-3
U: Proteasome subunit beta type-1
V: Proteasome subunit beta type-2
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-4
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-6
8: Proteasome subunit beta type-7
A: Proteasome subunit alpha type-6
B: Proteasome subunit alpha type-2
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-7
E: Proteasome subunit alpha type-5
F: Proteasome subunit alpha type-1
G: Proteasome subunit alpha type-3
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
H: 26S protease regulatory subunit 7
I: 26S protease regulatory subunit 4
K: 26S protease regulatory subunit 6B
L: 26S protease regulatory subunit 10B
M: 26S protease regulatory subunit 6A
J: 26S protease regulatory subunit 8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,049,26545
ポリマ－1,046,18034
非ポリマー3,08511
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
タイプ名称対称操作数
identity operation1_5551
Buried area170570 Å2
ΔGint-649 kcal/mol
Surface area300620 Å2
手法PISA

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要素

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Proteasome subunit alpha type- ... , 7種, 14分子 NAOBPCQDRESFTG

#1: 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: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P60900, proteasome endopeptidase complex
#2: 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: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P25787, proteasome endopeptidase complex
#3: 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: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P25789, proteasome endopeptidase complex
#4: 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: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: O14818, proteasome endopeptidase complex
#5: 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: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P28066, proteasome endopeptidase complex
#6: 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: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P25786, proteasome endopeptidase complex
#7: 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: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P25788, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 7種, 14分子 U1V2W3X4Y5Z687

#8: タンパク質 Proteasome subunit beta type-1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / ...Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


分子量: 26522.396 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P20618, proteasome endopeptidase complex
#9: タンパク質 Proteasome subunit beta type-2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


分子量: 22864.277 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PSMB2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P49721, proteasome endopeptidase complex
#10: タンパク質 Proteasome subunit beta type-3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


分子量: 22972.896 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P49720, proteasome endopeptidase complex
#11: タンパク質 Proteasome subunit beta type-4 / 26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex ...26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3


分子量: 29231.178 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P28070, proteasome endopeptidase complex
#12: タンパク質 Proteasome subunit beta type-5 / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / ...Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit MB1 / Proteasome subunit X


分子量: 28510.248 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P28074, proteasome endopeptidase complex
#13: タンパク質 Proteasome subunit beta type-6 / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / ...Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / Proteasome subunit Y


分子量: 25377.652 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P28072, proteasome endopeptidase complex
#14: タンパク質 Proteasome subunit beta type-7 / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


分子量: 30000.418 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q99436, proteasome endopeptidase complex

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

#15: 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: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P35998
#16: 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: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P62191
#17: 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: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P43686
#18: 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: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P62333
#19: 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: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P17980
#20: 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: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P62195

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非ポリマー , 3種, 11分子

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


分子量: 507.181 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C10H16N5O13P3 / コメント: ATP, エネルギー貯蔵分子*YM
#22: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


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


分子量: 427.201 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / コメント: ADP, エネルギー貯蔵分子*YM

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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

構成要素名称: human 26S proteasome / タイプ: COMPLEX / Entity ID: #1-#20 / 由来: NATURAL
分子量値: 2.5 MDa / 実験値: NO
由来(天然)生物種: Homo sapiens (ヒト)
緩衝液pH: 7.5
試料濃度: 0.5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: This sample was monodisperse.
急速凍結凍結剤: ETHANE

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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
撮影平均露光時間: 1.5 sec. / 電子線照射量: 45 e/Å2 / フィルム・検出器のモデル: OTHER / 撮影したグリッド数: 19 / 実像数: 40211

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解析

ソフトウェア名称: PHENIX / バージョン: (1.10.1_2155: ???) / 分類: 精密化
EMソフトウェア
ID名称バージョンカテゴリ
1TOM Toolbox粒子像選択
4CTFFIND4CTF補正
7MDFFモデルフィッティング
12RELION1.4３次元再構成
13PHENIXモデル精密化
画像処理詳細: Falcon III
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: 688742
3次元再構成解像度: 3.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 461402 / アルゴリズム: FOURIER SPACE / 対称性のタイプ: POINT
原子モデル構築プロトコル: FLEXIBLE FIT
精密化解像度: 3.9→3.9 Å / SU ML: 0.43 / σ(F): 1.36 / 位相誤差: 20.73 / 立体化学のターゲット値: MLHL
Rfactor反射数%反射
Rfree0.2053 105155 2.5 %
Rwork0.2033 --
obs0.2033 4203206 100 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.00768568
ELECTRON MICROSCOPYf_angle_d0.86792569
ELECTRON MICROSCOPYf_dihedral_angle_d15.61441790
ELECTRON MICROSCOPYf_chiral_restr0.04710403
ELECTRON MICROSCOPYf_plane_restr0.00611976
精密化 TLS

手法: refined / Refine-ID: ELECTRON MICROSCOPY

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.20450.5350.18922.30770.63733.1374-0.1961-0.64160.2190.4896-0.11080.3156-0.2573-0.26890.15230.37530.08580.07260.4738-0.04930.4306201.5406280.2895290.9689
22.5644-0.0731-1.16924.59191.00353.1042-0.2845-0.29260.52550.39250.11630.3047-0.36020.11120.14510.44930.1343-0.08380.2845-0.01340.509203.8203298.912266.9078
32.99890.352-0.73913.0051-0.68312.481-0.16960.10920.7193-0.13170.18890.4739-0.6295-0.28410.03780.48720.1109-0.12230.44710.05140.5345202.1466293.8148235.5695
44.7313-0.2267-0.07073.1286-0.17224.5496-0.06640.88960.5594-0.86120.136-0.03990.0661-0.2545-0.03340.4261-0.02620.01810.4640.09160.4755199.9678265.0411219.9153
53.17180.2656-0.3592.37241.10142.5571-0.18810.4137-0.3122-0.2506-0.10180.17860.1384-0.27970.30610.3867-0.0505-0.01450.43130.07060.4073199.5631236.9594235.0158
63.428-0.48380.30144.9839-1.0011.8456-0.3051-0.015-0.6324-0.16990.090.34050.4046-0.19980.24110.3662-0.0830.15840.4287-0.04150.4216199.2248229.1361265.5938
72.7855-0.07320.84093.4767-1.27843.9568-0.1772-0.3704-0.46570.66510.31750.5280.3596-0.4317-0.09380.49690.02770.21530.39680.0460.4743200.3577247.6836290.6389
84.5833-1.14810.41223.37490.52772.8696-0.6774-0.3608-0.83590.35130.3069-0.28650.91560.2579-0.05790.3225-0.3098-0.08690.2299-0.05180.3686240.2612224.089252.9601
94.9197-1.4684-2.28872.8332-1.38814.46960.04480.5815-0.2185-0.4269-0.0880.1671-0.1344-0.11710.1090.3768-0.0497-0.17810.29520.00420.3163241.121272.9841221.7282
104.34710.499-1.36755.97411.10642.2609-0.03740.12620.4516-0.2972-0.0925-0.0828-0.46850.07330.10110.48330.0636-0.12790.18080.12770.3691242.6118296.9367244.1567
115.17110.06381.46753.2888-1.00931.0671-0.1127-0.48-0.23120.3147-0.12420.0490.2390.22580.21570.4811-0.05090.16580.33430.01440.2377242.1811236.2752284.0675
124.8668-1.00590.331.8687-0.52124.2224-0.09220.1002-0.2427-0.07260.13080.0780.1071-0.1207-0.11850.1735-0.1784-0.07870.295-0.09770.382239.8196240.0624225.814
135.14561.11440.5362.2403-1.33453.1327-0.0863-0.35030.06010.3380.06570.0334-0.19730.02830.08290.41090.01380.18710.3122-0.1320.2754241.7602267.311294.3989
141.58570.2593-0.3281.37641.59643.19830.01210.18650.37690.17540.2402-0.0708-0.6199-0.069-0.15990.45430.0728-0.02730.3075-0.01190.4757243.0232296.0313272.0273
153.9587-0.5047-0.30313.7318-1.50712.033-0.6633-0.08750.7590.06290.51820.1914-0.6812-0.04770.00210.6434-0.45810.02470.3711-0.03080.5514277.0058297.2208252.361
165.5267-0.81072.11093.17720.88283.1451-0.05150.54350.2456-0.3132-0.0802-0.22680.2070.0520.08220.344-0.00660.21320.34220.02110.3022275.5012248.1928221.4816
174.49290.26081.84535.9246-0.15442.7412-0.04670.0689-0.3710.0563-0.1550.05920.27460.03780.26830.41520.13940.07560.2879-0.09220.3698274.4823224.3733244.1437
184.15460.0441-0.89122.88060.49592.2699-0.1669-0.78910.26890.2823-0.0408-0.1024-0.28130.15040.22820.5709-0.1768-0.09920.3428-0.10650.4055275.7463285.1688283.5982
194.8914-1.33410.4441.20760.71565.0539-0.03640.32750.4096-0.26320.0458-0.2175-0.17440.3264-0.08510.436-0.28560.10140.30750.10970.4644276.8336281.1676225.3296
203.84190.70910.08312.17421.55054.2042-0.1447-0.4121-0.07720.30120.0694-0.18170.06790.03970.05050.42790.03-0.22720.42530.09210.2997276.3172254.1606294.1522
211.34840.29770.41510.5844-0.93973.48390.04710.0895-0.33670.03630.0991-0.00090.42630.0635-0.14430.41640.2181-0.01850.3790.01220.5354274.6765225.3894271.983
223.250.4362-0.47022.1759-0.27463.3956-0.2282-0.4755-0.14420.64130.0172-0.57460.27720.48220.2110.61320.1484-0.21610.82970.03610.5872316.4957241.1359290.0806
233.36260.25550.59623.4378-0.38733.0434-0.1998-0.6107-0.53950.3939-0.0231-0.70840.42570.4310.20580.51830.1781-0.08190.71070.08620.5882313.6415222.3616266.1926
242.84270.56960.77932.69290.53882.8321-0.2010.0595-0.5916-0.15120.2667-0.68780.67780.5199-0.03050.61820.18350.10820.7074-0.04480.656314.7661227.376234.7848
253.9309-0.7469-0.60733.45170.40824.8012-0.13271.0323-0.3428-1.04910.2036-0.28110.08150.8328-0.05860.6958-0.15460.14450.8103-0.08380.66316.6206256.1289218.9618
264.097-0.7019-0.45622.797-0.40711.9342-0.14310.38930.4639-0.3688-0.0036-0.3983-0.35340.41710.12460.6908-0.24160.08880.7381-0.05790.5983317.3811284.2085233.8901
272.9309-0.4206-0.07433.7515-0.09842.019-0.1891-0.00020.8210.08350.0384-0.7289-0.51640.49880.1670.6634-0.3024-0.06470.7605-0.05020.7929318.2872292.2234264.239
282.4301-0.303-0.72282.50420.48322.7672-0.1166-0.45060.51770.60750.1522-0.6764-0.20410.6599-0.07490.6355-0.0809-0.25190.8709-0.07770.7323317.758273.7697289.3856
292.1970.0011-1.66032.22510.52286.0870.00160.1882-0.2536-0.09180.14390.63940.14-0.5538-0.16780.3155-0.0371-0.12550.67950.02610.7648163.1994247.7786249.4208
302.25730.4095-0.78665.1708-1.49744.26110.16610.42430.4277-0.276-0.39170.1723-0.2294-0.17290.15320.39730.1227-0.04210.77290.020.7576165.3044275.5338231.8285
311.47450.1272-0.23564.29461.81253.4080.02090.1430.1086-0.04510.0482-0.378-0.3802-0.0997-0.01180.61280.1285-0.03060.80430.23820.7693162.2371304.0736246.4576
322.82850.15271.76164.17820.07783.525-0.16030.11950.43460.41690.1706-0.0154-0.55360.3201-0.0490.8390.07840.14520.60230.05730.6255158.8472304.0257280.1538
331.1590.251-0.03273.68941.9153.1255-0.265-0.5966-0.03881.22790.3021-0.51380.2228-0.04880.07870.91570.213-0.22640.8536-0.02440.7506163.362277.2622297.2853
342.4509-2.5369-1.08844.83230.65022.7797-0.5108-0.2831-0.35630.65450.47630.15180.0829-0.31390.02740.6028-0.0494-0.06980.66830.13640.7458163.18248.3556282.3016
353.6287-1.0023-0.99540.90630.31285.47820.1640.5683-0.5543-0.74780.15430.70350.8093-0.3192-0.48431.6067-0.17240.28470.8927-0.10241.4913124.783258.5415259.3213
361.9726-1.1453-1.87571.02080.32412.56080.01130.7245-0.269-1.3314-0.1680.35550.6658-0.57980.06792.2435-0.31150.291.3464-0.14561.4124123.5468260.7508240.5954
370.6752-0.15770.76060.962-0.58552.9202-0.33290.51230.4008-0.22540.20320.23080.01-1.23630.12721.13750.0782-0.28231.1941-0.03011.1753111.8346298.6507250.3812
384.270.21770.5792.1111-0.55220.3954-0.6518-0.02640.3268-0.37860.50010.5768-0.8605-1.35930.08181.13920.4139-0.29541.40940.10620.993110.0627307.0162263.7915
390.88440.77-0.42161.8755-1.27943.7480.031-1.5284-0.43911.0665-0.11290.86380.9858-0.45550.19521.81270.14750.59361.81560.29961.3797115.3219276.6902303.9052
402.0450.95990.0680.947-1.13932.87370.1555-1.0307-0.47251.8885-0.54330.55280.5424-1.48190.2652.2441-0.22480.87342.08930.1991.3807115.1526268.0774307.6142
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1ELECTRON MICROSCOPY1chain A
2ELECTRON MICROSCOPY2chain B
3ELECTRON MICROSCOPY3chain C
4ELECTRON MICROSCOPY4chain D
5ELECTRON MICROSCOPY5chain E
6ELECTRON MICROSCOPY6chain F
7ELECTRON MICROSCOPY7chain G
8ELECTRON MICROSCOPY8chain 1
9ELECTRON MICROSCOPY9chain 2
10ELECTRON MICROSCOPY10chain 3
11ELECTRON MICROSCOPY11chain 4
12ELECTRON MICROSCOPY12chain 5
13ELECTRON MICROSCOPY13chain 6
14ELECTRON MICROSCOPY14chain 7
15ELECTRON MICROSCOPY15chain U
16ELECTRON MICROSCOPY16chain V
17ELECTRON MICROSCOPY17chain W
18ELECTRON MICROSCOPY18chain X
19ELECTRON MICROSCOPY19chain Y
20ELECTRON MICROSCOPY20chain Z
21ELECTRON MICROSCOPY21chain 8
22ELECTRON MICROSCOPY22chain N
23ELECTRON MICROSCOPY23chain O
24ELECTRON MICROSCOPY24chain P
25ELECTRON MICROSCOPY25chain Q
26ELECTRON MICROSCOPY26chain R
27ELECTRON MICROSCOPY27chain S
28ELECTRON MICROSCOPY28chain T
29ELECTRON MICROSCOPY29(chain H and resseq 161:433 ) or chain u
30ELECTRON MICROSCOPY30(chain I and resseq 170:434 ) or chain v
31ELECTRON MICROSCOPY31(chain J and resseq 133:397 ) or chain w
32ELECTRON MICROSCOPY32(chain K and resseq 152:411 ) or chain x
33ELECTRON MICROSCOPY33(chain L and resseq 117:379 ) or chain y
34ELECTRON MICROSCOPY34(chain M and resseq 170:431 ) or chain z
35ELECTRON MICROSCOPY35(chain H and resseq 1:160 )
36ELECTRON MICROSCOPY36(chain I and resseq 1:169 )
37ELECTRON MICROSCOPY37(chain J and resseq 1:132 )
38ELECTRON MICROSCOPY38(chain K and resseq 1:151 )
39ELECTRON MICROSCOPY39(chain L and resseq 1:116 )
40ELECTRON MICROSCOPY40(chain M and resseq 1:169 )

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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

他の情報も見る