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- PDB-8bzl: Human 20S Proteasome in complex with peptide activator peptide BLM42 -

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基本情報

登録情報
データベース: PDB / ID: 8bzl
タイトルHuman 20S Proteasome in complex with peptide activator peptide BLM42
要素
  • (Proteasome subunit alpha type- ...プロテアソーム) x 7
  • (Proteasome subunit beta type- ...プロテアソーム) x 7
  • ARG-SER-TYR-TYR-SER
キーワードHYDROLASE (加水分解酵素) / activator peptide / 20S proteasome (プロテアソーム) / protein degradation (タンパク質分解) / threonine protease
機能・相同性
機能・相同性情報


purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / proteasome core complex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex ...purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / proteasome core complex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / negative regulation of inflammatory response to antigenic stimulus / response to organonitrogen compound / sarcomere / proteasome complex / proteolysis involved in protein catabolic process / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / Degradation of AXIN / lipopolysaccharide binding / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / P-body / response to virus / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / 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 / nuclear matrix / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of NF-kappaB transcription factor activity / peptidase activity / ER-Phagosome pathway / regulation of inflammatory response / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / endopeptidase activity / response to oxidative stress / ficolin-1-rich granule lumen / nuclear body / リボソーム / Ub-specific processing proteases / cadherin binding / intracellular membrane-bounded organelle / 中心体 / シナプス / ubiquitin protein ligase binding / Neutrophil degranulation / ミトコンドリア / タンパク質分解 / RNA binding
類似検索 - 分子機能
Proteasome subunit alpha 1 / 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 subunit alpha 1 / 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 / Nucleophile aminohydrolases, N-terminal
類似検索 - ドメイン・相同性
: / Proteasome subunit alpha type-7 / 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 alpha type-7 / 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 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-7
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.14 Å
データ登録者Henneberg, F. / Chari, A. / Jankowska, E. / Witkowska, J.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: To Be Published
タイトル: Peptidic, Blm10-based activators of human 20S proteasome in vitro and in cellulo enhance degradation of proteins connected with neurodegeneration.
著者: Gizynska, M. / Karpowicz, P. / Sowik, D. / Trepczyk, K. / Witkowska, J. / Hennenberg, F. / Chari, A. / Gieldon, A. / Pierzynowska, K. / Gaffke, L. / Wegrzyn, G. / Jankowska, E.
履歴
登録2022年12月15日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年12月27日Provider: repository / タイプ: Initial release

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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
3: Proteasome subunit beta type-3
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-4
C: Proteasome subunit alpha type-7
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-1
F: Proteasome subunit alpha type-3
G: Proteasome subunit alpha type-6
H: Proteasome subunit beta type-7
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-2
K: Proteasome subunit beta type-5
L: Proteasome subunit beta type-1
M: Proteasome subunit beta type-4
N: Proteasome subunit beta 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 alpha type-6
V: Proteasome subunit beta type-7
X: Proteasome subunit beta type-2
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-1
a: Proteasome subunit beta type-4
b: Proteasome subunit beta type-6
c: ARG-SER-TYR-TYR-SER
d: ARG-SER-TYR-TYR-SER
e: ARG-SER-TYR-TYR-SER
f: ARG-SER-TYR-TYR-SER
g: ARG-SER-TYR-TYR-SER
h: ARG-SER-TYR-TYR-SER
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)777,602113
ポリマ－773,06634
非ポリマー4,53779
水61,7193426
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_555x,y,z1
Buried area128060 Å2
ΔGint-1125 kcal/mol
Surface area205730 Å2
手法PISA
単位格子
Length a, b, c (Å)113.915, 203.262, 316.421
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
113
213
323
423
533
633
743
843
953
1053
1163
1263
1373
1473
1583
1683
1793
1893
19103
20103
21113
22113
23123
24123
25133
26133
27143
28143

NCSドメイン領域:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
111131 - 204
211131 - 204
322133 - 229
422133 - 229
533132 - 243
633132 - 243
744132 - 229
844132 - 229
955139 - 238
1055139 - 238
1166134 - 236
1266134 - 236
1377136 - 243
1477136 - 243
1588134 - 243
1688134 - 243
1799131 - 220
1899131 - 220
191010131 - 196
201010131 - 196
211111131 - 198
221111131 - 198
231212131 - 213
241212131 - 213
251313131 - 213
261313131 - 213
271414131 - 196
281414131 - 196

NCSアンサンブル:
ID詳細
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28

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要素

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Proteasome subunit beta type- ... , 7種, 14分子 3IHVJXKYLZMaNb

#1: タンパク質 Proteasome subunit beta type-3 / PSMB3 / 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
#9: タンパク質 Proteasome subunit beta type-7 / プロテアソーム / 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
詳細: The structure shows the processed mature form of the sequence.
由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q99436, proteasome endopeptidase complex
#10: タンパク質 Proteasome subunit beta type-2 / PSMB2 / 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: 天然 / 詳細: Modified cysteine residue / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P49721, proteasome endopeptidase complex
#11: タンパク質 Proteasome subunit beta type-5 / PSMB5 / 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
詳細: The structure shows the processed mature form of the sequence.
由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P28074, proteasome endopeptidase complex
#12: タンパク質 Proteasome subunit beta type-1 / PSMB1 / 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
#13: タンパク質 Proteasome subunit beta type-4 / PSMB4 / 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
#14: タンパク質 Proteasome subunit beta type-6 / プロテアソーム / 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

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

#2: タンパク質 Proteasome subunit alpha type-2 / プロテアソーム / 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
#3: タンパク質 Proteasome subunit alpha type-4 / プロテアソーム / 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
#4: タンパク質 Proteasome subunit alpha type-7 / プロテアソーム / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


分子量: 27986.941 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: Modified cysteine residue / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: O14818
#5: タンパク質 Proteasome subunit alpha type-5 / プロテアソーム / 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
#6: タンパク質 Proteasome subunit alpha type-1 / プロテアソーム / 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: 29720.752 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: Modified cysteine residue / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P25786
#7: タンパク質 Proteasome subunit alpha type-3 / プロテアソーム / 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
#8: タンパク質 Proteasome subunit alpha type-6 / プロテアソーム / 27 kDa prosomal protein / PROS-27 / p27K / Macropain iota chain / Multicatalytic endopeptidase ...27 kDa prosomal protein / PROS-27 / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


分子量: 27614.635 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: modified cysteine residue / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P60900

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タンパク質・ペプチド , 1種, 6分子 cdefgh

#15: タンパク質・ペプチド
ARG-SER-TYR-TYR-SER


分子量: 1790.950 Da / 分子数: 6 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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非ポリマー , 5種, 3505分子

#16: 化合物...
ChemComp-CL / CHLORIDE ION / クロリド / 塩化物


分子量: 35.453 Da / 分子数: 54 / 由来タイプ: 合成 / 式: Cl
#17: 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: 10 / 由来タイプ: 合成 / 式: Mg
#18: 化合物
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / ペンタエチレングリコ-ル / ポリエチレングリコール


分子量: 238.278 Da / 分子数: 9 / 由来タイプ: 合成 / 式: C10H22O6 / コメント: 沈殿剤*YM
#19: 化合物
ChemComp-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 6 / 由来タイプ: 合成 / 式: K
#20: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 3426 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.37 Å3/Da / 溶媒含有率: 48.14 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: 0.1 M Bis-Tris, 0.2 M Magnesium Chloride, 10 % PEG3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: Y
放射光源由来: シンクロトロン / サイト: PETRA III, EMBL c/o DESY / ビームライン: P14 (MX2) / 波長: 0.9763 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2018年4月4日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9763 Å / 相対比: 1
反射解像度: 2.14→107.181 Å / Num. obs: 327921 / % possible obs: 94.5 % / 冗長度: 7.1 %
詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.995 / CC1/2 anomalous: -0.256 / Rmerge(I) obs: 0.1366 / Rpim(I) all: 0.055 / Rrim(I) all: 0.1474 / AbsDiff over sigma anomalous: 0.585 / Baniso tensor eigenvalue 1: 22.7677 Å2 / Baniso tensor eigenvalue 2: 3.451 Å2 / Baniso tensor eigenvalue 3: 0 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 2.395 Å / Aniso diffraction limit 2: 2.14 Å / Aniso diffraction limit 3: 2.248 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 6.65 / Num. measured all: 2327154 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 94.5 / % possible ellipsoidal: 94.5 / % possible ellipsoidal anomalous: 94.5 / % possible spherical: 81.6 / % possible spherical anomalous: 81.2 / Redundancy anomalous: 3.65 / Signal type: local
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
6.313-107.1816.960.06312.4111419611419616396163960.996-0.2520.02570.06820.27510099.810099.81003.7699.8
4.987-6.3136.940.078912.0211382411382416395163950.995-0.4390.03220.08540.39999.810099.810099.83.64100
4.346-4.9877.040.097412.2111537211537216397163970.992-0.430.03920.10510.46299.799.899.799.899.73.6699.8
3.941-4.3467.130.104511.9211687111687116396163960.99-0.3090.04170.11270.46799.399.799.399.799.33.799.7
3.655-3.9417.170.100811.3911762311762316395163950.993-0.1890.04030.10870.47299.799.999.799.999.73.7199.9
3.437-3.6557.210.117410.7411813411813416395163950.991-0.2080.04690.12660.52199.910099.910099.93.71100
3.263-3.4377.10.1449.6311636111636116398163980.99-0.2880.0580.15540.5691001001001001003.65100
3.119-3.2636.860.17218.3411247411247416395163950.986-0.2170.07070.18630.62499.910099.910099.93.53100
2.998-3.1196.850.19727.2411236011236016395163950.982-0.1790.08080.21340.66399.610099.610099.63.52100
2.893-2.9986.910.22826.3911334811334816400164000.981-0.1540.09290.24660.65999.699.999.699.999.63.5599.9
2.802-2.8936.960.2765.5211405311405316396163960.975-0.1260.1120.29820.67499.699.999.699.999.63.5799.9
2.72-2.8026.980.33514.6711446811446816394163940.965-0.0490.13560.36180.67298.899.198.899.198.83.5799.1
2.646-2.727.060.40964.0911572011572016397163970.95-0.0370.16510.4420.69897.497.497.497.497.43.697.4
2.579-2.6467.120.47683.5811668511668516393163930.941-0.0260.19140.51420.67796.296.196.296.196.23.6396.1
2.517-2.5797.150.59062.9711729111729116396163960.91-0.0270.23680.63680.64995.395.195.395.195.33.6595.1
2.46-2.5177.20.68182.6211798511798516397163970.882-0.0180.27270.73480.64394.293.894.293.894.23.6793.8
2.407-2.467.220.86722.1911837111837116397163970.8330.0170.34620.93440.6692.692.292.692.292.63.6892.2
2.355-2.4077.310.98971.8911990011990016398163980.794-0.0140.39261.06550.61589.489.189.487.287.53.7389.1
2.295-2.3557.351.16721.6712057012057016394163940.72-0.0020.46151.2560.62679.980.279.968.2683.7680.2
2.14-2.2957.411.41841.5312154812154816397163970.635-0.0120.55851.52540.62363.762.963.721.721.63.7962.9
Serial crystallography sample delivery手法: fixed target

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0352精密化
autoPROC1.0.5 20220608data processing
XDSJan 10, 2022データ削減
Aimless0.7.8データスケーリング
Coot0.9.8.2モデル構築
MOLREP位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.14→107.123 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.216 / SU B: 13.54 / SU ML: 0.172 / Average fsc free: 0.9609 / Average fsc work: 0.9696 / 交差検証法: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.213 / 詳細: Hydrogens have not been used
Rfactor反射数%反射Selection details
Rfree0.2261 16354 4.987 %RANDOM
Rwork0.1962 311565 --
all0.198 ---
obs-327919 81.566 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK BULK SOLVENT
原子変位パラメータBiso mean: 47.647 Å2
Baniso -1Baniso -2Baniso -3
1--0.295 Å2-0 Å20 Å2
2--0.477 Å2-0 Å2
3----0.182 Å2
精密化ステップサイクル: LAST / 解像度: 2.14→107.123 Å
タンパク質核酸リガンド溶媒全体
原子数47032 0 236 3404 50672
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01248329
X-RAY DIFFRACTIONr_angle_refined_deg0.8921.64765442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11856187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.525.118338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.254108026
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.107102038
X-RAY DIFFRACTIONr_chiral_restr0.0740.27415
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0235935
X-RAY DIFFRACTIONr_nbd_refined0.1930.221627
X-RAY DIFFRACTIONr_nbtor_refined0.2960.233299
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.22873
X-RAY DIFFRACTIONr_metal_ion_refined0.0470.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.212
X-RAY DIFFRACTIONr_mcbond_it0.662.05424682
X-RAY DIFFRACTIONr_mcangle_it1.1883.07330798
X-RAY DIFFRACTIONr_scbond_it0.8262.16423647
X-RAY DIFFRACTIONr_scangle_it1.3713.19734613
X-RAY DIFFRACTIONr_lrange_it6.9131.62373080
X-RAY DIFFRACTIONr_ncsr_local_group_10.0550.056372
X-RAY DIFFRACTIONr_ncsr_local_group_20.050.056305
X-RAY DIFFRACTIONr_ncsr_local_group_30.050.056914
X-RAY DIFFRACTIONr_ncsr_local_group_40.0820.056389
X-RAY DIFFRACTIONr_ncsr_local_group_50.0490.056469
X-RAY DIFFRACTIONr_ncsr_local_group_60.0510.057079
X-RAY DIFFRACTIONr_ncsr_local_group_70.0620.057370
X-RAY DIFFRACTIONr_ncsr_local_group_80.0660.056944
X-RAY DIFFRACTIONr_ncsr_local_group_90.0610.056597
X-RAY DIFFRACTIONr_ncsr_local_group_100.0460.056417
X-RAY DIFFRACTIONr_ncsr_local_group_110.0420.056277
X-RAY DIFFRACTIONr_ncsr_local_group_120.0430.056612
X-RAY DIFFRACTIONr_ncsr_local_group_130.0410.056794
X-RAY DIFFRACTIONr_ncsr_local_group_140.020.056068
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)Weight position
113X-RAY DIFFRACTIONLocal ncs0.054660.05011
123X-RAY DIFFRACTIONLocal ncs0.054660.05011
233X-RAY DIFFRACTIONLocal ncs0.049640.0501
243X-RAY DIFFRACTIONLocal ncs0.049640.0501
353X-RAY DIFFRACTIONLocal ncs0.050060.05011
363X-RAY DIFFRACTIONLocal ncs0.050060.05011
473X-RAY DIFFRACTIONLocal ncs0.081660.05011
483X-RAY DIFFRACTIONLocal ncs0.081660.05011
593X-RAY DIFFRACTIONLocal ncs0.048830.05011
5103X-RAY DIFFRACTIONLocal ncs0.048830.05011
6113X-RAY DIFFRACTIONLocal ncs0.051250.05011
6123X-RAY DIFFRACTIONLocal ncs0.051250.05011
7133X-RAY DIFFRACTIONLocal ncs0.06210.05011
7143X-RAY DIFFRACTIONLocal ncs0.06210.05011
8153X-RAY DIFFRACTIONLocal ncs0.066280.0501
8163X-RAY DIFFRACTIONLocal ncs0.066280.0501
9173X-RAY DIFFRACTIONLocal ncs0.061240.0501
9183X-RAY DIFFRACTIONLocal ncs0.061240.0501
10193X-RAY DIFFRACTIONLocal ncs0.045630.05011
10203X-RAY DIFFRACTIONLocal ncs0.045630.05011
11213X-RAY DIFFRACTIONLocal ncs0.042340.05011
11223X-RAY DIFFRACTIONLocal ncs0.042340.05011
12233X-RAY DIFFRACTIONLocal ncs0.042850.0501
12243X-RAY DIFFRACTIONLocal ncs0.042850.0501
13253X-RAY DIFFRACTIONLocal ncs0.04060.05011
13263X-RAY DIFFRACTIONLocal ncs0.04060.05011
14273X-RAY DIFFRACTIONLocal ncs0.019990.05011
14283X-RAY DIFFRACTIONLocal ncs0.019990.05011
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.14-2.1960.2951070.28622400.287294950.9430.9437.95730.289
2.196-2.2560.3113090.29158320.292287560.9340.94221.35550.292
2.256-2.3210.3037470.294136460.294279890.9370.94251.42380.293
2.321-2.3920.29610630.277206760.278271510.9430.9580.0670.273
2.392-2.4710.28512220.262230470.263264120.9450.95591.88630.256
2.471-2.5580.26212070.242228590.243254720.9550.96294.48020.233
2.558-2.6540.26711610.223225120.225246810.9540.96895.91590.212
2.654-2.7620.25311140.218220810.219236940.9580.9797.8940.207
2.762-2.8850.25411650.214215440.216227410.9590.97199.85930.204
2.885-3.0260.24611130.208207120.21218450.960.97399.90840.203
3.026-3.1890.22810860.198196390.2207250.9680.9761000.2
3.189-3.3830.22710050.189186860.191196910.970.9791000.198
3.383-3.6160.219720.183175110.184184830.9750.9821000.199
3.616-3.9050.2168570.174164020.176172810.9740.98399.87270.197
3.905-4.2770.1967830.168150690.17158900.9770.98399.76090.199
4.277-4.7810.1857000.16137110.161144600.9790.98499.66110.201
4.781-5.5190.2136220.171121710.173128000.9730.98299.94530.22
5.519-6.7550.2344800.21104260.211109060.970.9751000.266
6.755-9.5340.1844100.16981310.1785410.9830.9851000.23
9.534-107.1230.2112310.21346690.21349350.9710.96899.29080.302
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

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)
11.39590.43540.49842.0105-0.13761.9961-0.00940.14480.05-0.2806-0.1023-0.42920.15550.59210.11170.23120.13420.12910.27740.06450.20976.3296206.35471.1938
21.2519-0.24090.06681.8224-0.21271.1223-0.05010.3009-0.1184-0.3623-0.0482-0.32210.36660.35480.09830.59240.11140.06880.1821-0.0310.209862.794178.27450.4845
32.01040.0566-0.04053.0502-0.1411.8963-0.08490.0306-0.4869-0.27130.0828-0.02020.5278-0.05520.00210.6344-0.1229-0.11210.2328-0.0150.269332.7551170.8208-3.2512
40.176-0.1297-0.4030.6630.10081.2548-0.00510.1863-0.134-0.2877-0.06110.13560.2096-0.40020.06630.5353-0.162-0.23340.59580.02680.40998.8943189.2794-7.0666
52.09020.11440.34210.8097-0.11721.47680.03150.1627-0.2725-0.22250.06870.27060.2083-0.4861-0.10010.2595-0.1323-0.19290.29490.11340.27549.7322220.9804-8.7179
61.8698-0.77460.00171.6484-0.13831.27630.03910.14380.1853-0.1988-0.05910.1276-0.0663-0.14770.020.1195-0.0401-0.09050.0920.1020.1932.5809240.5121-7.658
70.89550.08820.13112.06780.39011.18890.00790.23940.1994-0.402-0.0593-0.1608-0.07950.31820.05140.141-0.00550.05640.19940.13490.179263.9215233.4074-3.5982
80.11620.0123-0.0641.9906-0.21740.8104-0.0076-0.0176-0.12010.125-0.0984-0.1950.08380.36530.1060.06890.00130.01430.21860.06210.198271.4185213.981939.5416
90.61920.19250.66561.1231-0.78081.93050.04890.0625-0.0316-0.0895-0.1434-0.09270.15580.40380.09440.18050.07620.03080.15680.05430.144466.0294186.602539.8004
101.08020.68290.08730.9537-0.49752.6402-0.05510.0794-0.0221-0.20690.03640.19010.513-0.17540.01870.3636-0.0339-0.05360.0341-0.00390.171438.2087170.408936.6901
111.2296-0.0274-0.82491.3666-0.12852.159-0.03340.1915-0.0317-0.20420.04490.19760.3643-0.3889-0.01150.2252-0.2107-0.1470.24160.11740.27417.1058181.60432.8384
121.07960.0593-0.55311.36420.41641.21750.024-0.03630.1312-0.12060.03330.3442-0.0245-0.4743-0.05730.0756-0.0858-0.09720.40790.19080.3513-1.9011211.292531.1523
131.33540.30210.14131.25130.25741.9398-0.0348-0.01350.21150.05510.09550.245-0.3344-0.3213-0.06070.08290.06110.02060.15810.13930.263916.5752238.53132.9165
141.3408-0.3750.29240.97460.17782.79430.04560.02950.07950.0137-0.05880.0072-0.36210.19340.01330.1222-0.06520.01260.04780.03080.141548.9393241.510334.9413
150.8956-0.1620.39931.2381-0.13391.8724-0.0282-0.11390.18180.14970.00250.368-0.3262-0.48540.02580.33540.09010.2750.49210.03410.4533-6.2239226.305103.1502
161.39990.40930.12451.27450.23091.079-0.0337-0.240.05870.21550.02980.3777-0.0632-0.520.00380.2595-0.04580.230.50440.10910.4058-7.0315196.1624104.9976
172.37230.1309-0.1422.18250.09051.99870.03640.0065-0.46090.1446-0.00090.33960.4418-0.3269-0.03550.4075-0.09140.11380.31030.12070.331516.4031176.7283109.1384
180.53610.3458-0.29081.11650.14761.6618-0.1147-0.1925-0.13060.39010.07460.14960.166-0.00950.04010.44010.03790.08110.26210.0990.232745.5751182.0188113.116
191.2992-0.66240.29861.5965-0.33721.6552-0.0157-0.3025-0.13010.26480.024-0.10160.01150.2944-0.00830.4083-0.1583-0.0460.24490.04550.144559.1112210.5579114.2034
202.22880.31540.12191.30350.21161.04460.124-0.34760.16440.207-0.103-0.1531-0.34810.1704-0.02110.6035-0.12930.08210.1696-0.04770.165447.4902238.5728111.4673
211.18650.3406-0.12461.3961-0.18650.8969-0.0001-0.24450.34210.325-0.04120.138-0.4339-0.19090.04130.61460.09160.21450.2981-0.07650.36817.2447245.2205107.3774
220.70360.550.07771.3951-0.18890.56920.00230.020.04560.08450.08930.2951-0.1927-0.3749-0.09160.20410.10470.17860.36570.08370.37991.3619231.604265.4797
230.62970.02580.76521.11030.46141.57670.0013-0.07440.0658-0.01680.05660.2796-0.1182-0.4349-0.05780.1082-0.03930.09570.45540.16410.4154-6.3869204.309465.6301
240.5634-0.25580.10680.8370.33962.3727-0.0462-0.0929-0.060.04340.10680.08130.4079-0.1592-0.06060.2073-0.15060.00230.1910.0990.288710.8112177.56569.3041
251.37770.1318-0.57071.37840.16642.1463-0.0243-0.18280.01040.1136-0.023-0.00440.39660.06090.04730.2157-0.0086-0.02810.03050.02560.128143.5053173.269173.1333
260.8754-0.0586-0.44421.6498-0.08461.48810.0396-0.03030.0260.0817-0.1342-0.23110.07950.42660.09460.0954-0.0116-0.0160.15840.06020.149565.2271195.827974.1044
271.3035-0.1704-0.11721.5956-0.45831.63790.02180.01160.11830.1622-0.0928-0.169-0.28370.29370.0710.1805-0.1199-0.00080.09190.00790.124660.9405228.552771.3873
281.6498-0.03110.0160.95760.02671.97140.016-0.02460.11250.245-0.01290.1699-0.4225-0.1213-0.00310.30270.02680.08750.04730.00740.184333.2309245.825968.8885
297.983-9.847-1.728712.6283.46954.1507-0.05250.0187-0.0577-0.04940.09680.0448-0.27030.1878-0.04420.283-0.04360.04350.34680.01150.30776.4178188.6707116.2545
304.8736-2.8675-1.90221.68821.11980.7436-0.00840.1586-0.1350.0092-0.0660.07660.0163-0.0490.07450.3873-0.0082-0.02450.30520.00430.375447.0468177.0476-10.8326
316.83427.7103-3.00949.4318-3.96592.1438-0.21690.1756-0.33620.13840.3683-0.00870.11640.0022-0.15150.5740.1330.13720.4516-0.02460.5302-5.128209.1819113.6098
329.2907-10.7059-0.323113.844-1.27171.8597-0.3781-0.74990.15910.14260.5212-0.04810.20320.5106-0.14310.3703-0.1214-0.02590.4731-0.01810.411714.183207.1582-15.0754
精密化 TLSグループSelection: ALL

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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