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- PDB-6vie: Structure of caspase-1 in complex with gasdermin D -

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基本情報

登録情報
データベース: PDB / ID: 6vie
タイトルStructure of caspase-1 in complex with gasdermin D
要素
  • Caspase-1 subunit p10
  • Caspase-1 subunit p20
  • Gasdermin-D
キーワードIMMUNE SYSTEM / dual site recognition
機能・相同性
機能・相同性情報


Release of apoptotic factors from the mitochondria / Pyroptosis / pyroptotic cell death / Regulation of TLR by endogenous ligand / caspase-1 / protease inhibitor complex / Interleukin-1 processing / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex ...Release of apoptotic factors from the mitochondria / Pyroptosis / pyroptotic cell death / Regulation of TLR by endogenous ligand / caspase-1 / protease inhibitor complex / Interleukin-1 processing / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / canonical inflammasome complex / pore complex assembly / positive regulation of interleukin-18 production / wide pore channel activity / CARD domain binding / cytokine precursor processing / NLRP3 inflammasome complex / phosphatidic acid binding / osmosensory signaling pathway / Interleukin-1 processing / cardiolipin binding / Interleukin-37 signaling / positive regulation of tumor necrosis factor-mediated signaling pathway / phosphatidylinositol-4-phosphate binding / pattern recognition receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / signaling receptor ligand precursor processing / phosphatidylserine binding / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / cytokine binding / protein autoprocessing / The NLRP3 inflammasome / protein secretion / Pyroptosis / Purinergic signaling in leishmaniasis infection / phosphatidylinositol-4,5-bisphosphate binding / Neutrophil degranulation / protein maturation / positive regulation of interleukin-1 beta production / cellular response to mechanical stimulus / NOD1/2 Signaling Pathway / protein homooligomerization / mitochondrial membrane / cellular response to type II interferon / kinase binding / positive regulation of inflammatory response / SARS-CoV-1 activates/modulates innate immune responses / cellular response to lipopolysaccharide / regulation of inflammatory response / regulation of apoptotic process / endopeptidase activity / defense response to Gram-negative bacterium / defense response to virus / microtubule / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / cysteine-type endopeptidase activity / apoptotic process / nucleolus / signal transduction / protein-containing complex / proteolysis / extracellular space / nucleoplasm / identical protein binding / plasma membrane / cytoplasm / cytosol
類似検索 - 分子機能
Gasdermin / Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain / Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain ...Gasdermin / Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain / Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Caspase-1 / Gasdermin-D
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.4 Å
データ登録者Liu, Z. / Xiao, T.S.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127609 米国
引用ジャーナル: Immunity / 年: 2020
タイトル: Caspase-1 Engages Full-Length Gasdermin D through Two Distinct Interfaces That Mediate Caspase Recruitment and Substrate Cleavage.
著者: Liu, Z. / Wang, C. / Yang, J. / Chen, Y. / Zhou, B. / Abbott, D.W. / Xiao, T.S.
履歴
登録2020年1月13日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年7月1日Provider: repository / タイプ: Initial release
改定 1.12020年7月29日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.page_first
改定 1.22023年10月11日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Caspase-1 subunit p20
B: Caspase-1 subunit p10
C: Gasdermin-D
D: Gasdermin-D


分子量 (理論値)分子数
合計 (水以外)133,6024
ポリマ－133,6024
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-42 kcal/mol
Surface area53670 Å2
単位格子
Length a, b, c (Å)138.500, 202.610, 124.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSER(chain 'C' and (resid 3 through 95 or resid 117...CC3 - 694 - 70
12VALVALVALVAL(chain 'C' and (resid 3 through 95 or resid 117...CC83 - 9584 - 96
13ALAALAILEILE(chain 'C' and (resid 3 through 95 or resid 117...CC117 - 173118 - 174
14METMETGLUGLU(chain 'C' and (resid 3 through 95 or resid 117...CC206 - 242207 - 243
15ASPASPARGARG(chain 'C' and (resid 3 through 95 or resid 117...CC288 - 451265 - 428
16VALVALGLNGLN(chain 'C' and (resid 3 through 95 or resid 117...CC454 - 484431 - 461
27SERSERSERSER(chain 'D' and (resid 3 through 451 or resid 454 through 484))DD3 - 694 - 70
28VALVALVALVAL(chain 'D' and (resid 3 through 451 or resid 454 through 484))DD83 - 9584 - 96
29ALAALAILEILE(chain 'D' and (resid 3 through 451 or resid 454 through 484))DD117 - 173118 - 174
210METMETGLUGLU(chain 'D' and (resid 3 through 451 or resid 454 through 484))DD206 - 242207 - 243
211ASPASPARGARG(chain 'D' and (resid 3 through 451 or resid 454 through 484))DD288 - 451265 - 428
212VALVALGLNGLN(chain 'D' and (resid 3 through 451 or resid 454 through 484))DD454 - 484431 - 461

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要素

#1: タンパク質 Caspase-1 subunit p20 / CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta- ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta-converting enzyme / p45


分子量: 21561.842 Da / 分子数: 1 / 断片: residues 120-316 / 変異: C285A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CASP1, IL1BC, IL1BCE / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P29466, caspase-1
#2: タンパク質 Caspase-1 subunit p10 / CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta- ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta-converting enzyme / p45


分子量: 10402.885 Da / 分子数: 1 / 断片: residues 317-404 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CASP1, IL1BC, IL1BCE / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P29466, caspase-1
#3: タンパク質 Gasdermin-D / Gasdermin domain-containing protein 1


分子量: 50818.738 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Gsdmdc1, Gsdmd / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9D8T2

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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: 3.3 Å3/Da / 溶媒含有率: 62.69 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 / 詳細: 0.2 M Ammonium citrate tribasic pH 7.0, 20% PEG3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-E / 波長: 0.979 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年6月19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: 0.979 Å / 相対比: 1
反射解像度: 3.4→78.52 Å / Num. obs: 24394 / % possible obs: 99.9 % / 冗長度: 6.906 % / Biso Wilson estimate: 151.63 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Χ2: 1.082 / Net I/σ(I): 16.69
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.4-3.496.9062.07117680.40.8532.2499.3
3.49-3.586.821.4191.5217080.5381.53899.8
3.58-3.696.3071.0042.1317130.7111.09699.9
3.69-3.87.3390.7943.0316320.8320.854100
3.8-3.937.3460.6053.9815960.910.651100
3.93-4.067.3160.425.4315460.9540.452100
4.06-4.227.2570.2857.8314910.9790.30799.9
4.22-4.397.0290.18111.5214380.9910.196100
4.39-4.587.1410.1381513850.9940.149100
4.58-4.817.0130.10718.4213130.9960.11599.9
4.81-5.076.8360.10119.0712580.9950.1199.9
5.07-5.386.2320.09718.7612100.9940.10699.9
5.38-5.756.8770.08721.8511110.9960.094100
5.75-6.217.270.07126.1410550.9980.07799.9
6.21-6.87.0910.05433.919720.9980.058100
6.8-7.66.7590.04340.78850.9990.046100
7.6-8.786.6570.02953.697940.9990.03199.9
8.78-10.755.810.02359.656680.9990.02599.4
10.75-15.216.5060.02167.275340.9990.023100
15.21-78.525.6470.0264.1531710.02298.8

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位相決定

位相決定手法: 分子置換
Phasing MR
最高解像度最低解像度
Rotation3.5 Å114.34 Å
Translation3.5 Å114.34 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER2.8.3位相決定
精密化構造決定の手法: 分子置換
開始モデル: 6N9N,6BZ9

6n9n

6bz9


解像度: 3.4→78.52 Å / SU ML: 0.5585 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 33.834
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.3143 1237 5.07 %
Rwork0.2877 23141 -
obs0.289 24378 99.82 %
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
原子変位パラメータBiso mean: 190.89 Å2
精密化ステップサイクル: LAST / 解像度: 3.4→78.52 Å
タンパク質核酸リガンド溶媒全体
原子数8038 0 0 0 8038
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00298171
X-RAY DIFFRACTIONf_angle_d0.781311060
X-RAY DIFFRACTIONf_chiral_restr0.04421294
X-RAY DIFFRACTIONf_plane_restr0.00441415
X-RAY DIFFRACTIONf_dihedral_angle_d20.48031078
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.540.39031390.36752523X-RAY DIFFRACTION99.29
3.54-3.70.37111320.35162525X-RAY DIFFRACTION99.85
3.7-3.890.31541370.33452548X-RAY DIFFRACTION99.93
3.89-4.140.3241230.31112554X-RAY DIFFRACTION100
4.14-4.460.27981380.27432562X-RAY DIFFRACTION99.96
4.46-4.90.30181310.2642563X-RAY DIFFRACTION99.93
4.9-5.610.31881500.30742575X-RAY DIFFRACTION99.93
5.61-7.070.35941440.3292586X-RAY DIFFRACTION99.96
7.07-78.520.29271430.25652705X-RAY DIFFRACTION99.58
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)
19.703261157171.465516498992.806580650032.51646850139-3.7377374838.50066338747-1.65690796161-3.46543343472-1.20810295382-1.37568687610.380585736825-0.5726938860362.69875032528-2.74424239759-0.4059259620791.831197397410.476270960916-0.544582630991.09100623908-0.3478863141471.6735777166111.2186697821-7.80446981275-35.1504558508
22.01211492047-0.383858908637-2.261579244379.034952180232.633117011019.202094092510.367267730593-0.3570901148020.641341689675-0.05484436876610.166875444259-2.429681932741.59425391.42101470238-0.5857029479691.242382590620.3206560358190.2680697008592.030578530380.2290519056511.3976273869618.66992784651.57281170816-41.7472193797
38.895428471131.35979372805-0.4108469100526.077124748653.522298339082.228377376491.23740602993-2.29388807694-0.609466297582.46058722923-0.503457299528-1.474994837820.729986786698-0.224008793179-0.5520088866471.21178028367-0.382038840784-0.1239759309911.800415037480.09529702589581.2898152514222.167787757718.6721074635-22.4481185981
46.647614231151.048636355792.752792882442.425854494272.307153190117.263960126180.587228523664-0.634972446731.318349266090.789072427044-1.24665122459-0.164942780201-1.04720652052.415822999830.2820931193181.3017947083-0.55589986661-0.08317643778981.965466086720.4872171816681.2863118074723.911812408917.0427752503-30.502447572
53.425291668470.650123972112-1.305858317927.30400203344-3.327463662516.88076892578-0.101738122459-0.0274762305374-0.442097502097-0.718972408413-0.970097025435-2.411393232790.2533400802052.42891388591.044101098590.884325877706-0.1462125456930.1223648005311.689253103940.3983406459341.1302116257720.001257659518.674357565-37.7430663787
63.28554474542.14338736979-3.829102466381.62384254315-2.766552041434.848315842840.9651349972750.484085726807-0.3963748498072.18946324250.670265043347-2.39178237993-1.322692426111.20152356929-1.631352059671.60406129066-0.397781150995-0.1408852356891.29890415422-0.05628582757972.0594357790112.851559901932.8294285191-23.599356847
74.513538166673.88496441883.645784559043.491754315773.527932419783.714996340030.5644087981080.196213359857-0.756738495077-1.262328396890.3003233456310.257077085551-0.4914335213740.7476927038041.511966148013.72172080552-1.97482606409-1.607283577850.700692940867-0.4759434646810.2469349793519.3506471911625.5605870492-34.8606637164
88.83748676538-3.96649974229-0.3874430645266.021687545985.666519972267.304595608322.604572017870.8670444341471.42955862944-1.31271474276-0.327307803869-2.18755221084-1.64726397709-2.25100003499-1.65666701741.14755585818-0.005129893896670.2625145606281.043743053770.01989327375161.395140220679.3536922482318.1359379259-32.9793885128
92.642195745642.12389783586-0.8977235387019.67321384527-3.08755015310.9369343432470.4385818457080.0364139791513-0.731612806355-0.6803265144190.7117999901191.251189882631.617452569082.344731530510.370352524612.90499560696-0.715822262587-0.1270148307191.991581650250.3295933264271.07646593072-13.883604881510.1672170768-0.0272464221998
108.04903348206-0.0149742187617-3.573386416662.53114952206-2.83957528974.80415120441-0.306204562536-1.55904975154-2.966880801720.347986685526-0.926004035652.08174465441-0.552167352982-0.5984367909920.3792608128481.15153863624-0.313687944366-0.5024371442251.357244142380.4453781642391.20757377893-17.63345399148.1199343651117.1168632663
116.850070549670.513586620032-0.4732761082574.545265878580.770902334394.322720509770.258103590628-1.128215464070.708185899740.420073254466-0.294435694337-0.1960805287330.117771692480.28875710092-0.022022129420.946159417995-0.270572686855-0.0607609719891.16135515253-0.001909574433421.502359365489.8435881768812.7898995641-26.5470440517
127.31353697987-5.30695249346-5.834727910864.061703567975.311830030151.99035194851-0.3415129133820.482809143974-0.355198357230.293167410302-0.3732460045822.820148166962.59206954287-2.89938563042-0.4021573193180.478157667711-0.120530418087-0.272299419661.52481794947-0.143506998921.802190943294.908077524443.9767423087-25.2967479107
130.82321384167-0.988364275133-0.08186573101675.96638713751-0.7259922231037.439635108610.695317150644-1.30290537953-0.4623133966280.407683915562-0.0481981512151-0.2732263394490.1281782822331.11902750895-0.4548532195470.581826759875-0.299823606068-0.09204445981151.565227876660.2738405955171.343600745216.201357875098.45561503139-26.6534513949
147.022318726472.90411731083-3.379607890328.38505064933-0.7422274838087.354947159610.904463397196-2.169509798642.20379736482.448848436250.110297206481-0.691369499742-1.64559784493-1.04743989186-1.395709588671.519850225430.2826721764320.2450242338781.624889547230.08620833064181.7085675434315.868386705847.48980088824.873916382
157.01672389932-1.59393515004-1.266439801718.57292926765-1.007495151069.309434233460.1721469511530.4490486145080.3098930295620.738774008045-0.638052533283-1.166907871010.3220390776940.8249734470860.4644818838711.07062376043-0.193716738464-0.1791885760411.50204220990.04564987303361.4349269400721.785093783736.576204619622.9382753237
163.410879364361.263700628130.2835389613721.217959398261.461397121671.79063890364-0.5691395717722.681215455830.418459567604-0.03708792017390.659978154406-0.405357305986-0.0107431456291-0.126628176824-0.2957020276151.8263922246-0.4789099568370.5591712851592.84730184308-0.1515934786161.440914730039.3362415801330.2141188142-3.33507631355
174.442315121091.61133867703-0.7309346644135.791197575094.605633994114.283199806350.259255530738-1.23980516954-0.5208485600512.05155695681-0.5340303442580.7478435140010.0219441318509-0.1559488210430.0549279926841.78497373338-0.07851662727050.1076524116141.925921582780.07327172958491.00061559445-3.4970656537325.20761192338.07815832316
183.15044229207-2.629612458591.650456884968.18905965842-1.852446571614.11469523606-0.2891531508770.2093413558250.154703475861.918610067890.3213663132740.651803566476-3.48472210222-0.5964045144090.002963169269612.51172246223-0.1138817814910.4528733313421.5691111709-0.2830659993811.71939728481-2.5545353237550.72473284225.13920937745
192.90051424678-0.9500671968411.582582144833.697821897122.277724442093.072811657360.5455615711780.0285909579564-0.3338963307540.0938011956966-0.6965776228130.5396661758110.09209576720470.121957716376-0.2197802436291.10015438869-0.2431120214760.01714138578822.04244928813-0.05015773849541.3363816854937.632579739463.279106821313.8643379353
202.45794688913-2.263480132220.7550540809128.664598207172.515611193433.57114741478-0.230892387893-0.3804949489450.02908864802060.655899718261-0.4692807192730.894525704132-0.699389104203-0.6800723441740.8258696425481.68151676309-0.84101705876-0.2377192996511.84880211498-0.1645172164281.4896936505231.555596086177.002656646718.4170564167
212.623689553920.3655720359312.740319667888.95501157251.676645333187.363864928920.0383426460932-1.285335161780.740862599360.7354011874510.6237956789080.251695984154-1.5020799683-0.3267645288590.4607047463521.34550230841-0.9249895926530.2893896412082.1351754236-0.4746650043971.3243935005431.918512243771.19960951215.5485573529
222.864148316830.0378494898179-2.740037354745.464222619950.5537157811312.45186824044-1.07878134868-0.551535640056-1.04155769382-1.088240690480.892670885742-0.816125973498-0.22211245709-0.279337299310.1885171376732.0548810587-0.592279629573-0.2754571730391.80299209043-0.3202837863291.1138212706133.207259959378.0148588794-13.116893213
234.28866647105-0.287334470313-2.849594717564.91363391284-4.655679723941.99359921906-2.11012323551.64438689899-0.260207654480.922157441585-1.72765332937-1.255753109313.20115185404-0.2046777819880.006562256300292.70684263925-1.69937491769-1.130121940140.350366350650.3320931223053.1017888402726.640949861852.1705023093-10.8203667633
244.620540938760.0463501973257-1.429670187784.673849873941.022205214073.75600981658-0.959689832845-0.217446724213-1.27647995024-0.5612593696630.166742530798-1.324695756930.717644358464-2.857921982361.231379783342.22804004963-0.6826969118190.7572122756871.769177884810.03886804592382.1578324612233.482736163658.7713853055-10.4106451847
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 131 through 151 )
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 163 )
3X-RAY DIFFRACTION3chain 'A' and (resid 164 through 195 )
4X-RAY DIFFRACTION4chain 'A' and (resid 196 through 207 )
5X-RAY DIFFRACTION5chain 'A' and (resid 208 through 235 )
6X-RAY DIFFRACTION6chain 'A' and (resid 236 through 254 )
7X-RAY DIFFRACTION7chain 'A' and (resid 255 through 264 )
8X-RAY DIFFRACTION8chain 'A' and (resid 265 through 293 )
9X-RAY DIFFRACTION9chain 'A' and (resid 294 through 307 )
10X-RAY DIFFRACTION10chain 'A' and (resid 308 through 316 )
11X-RAY DIFFRACTION11chain 'B' and (resid 317 through 362 )
12X-RAY DIFFRACTION12chain 'B' and (resid 363 through 376 )
13X-RAY DIFFRACTION13chain 'B' and (resid 377 through 404 )
14X-RAY DIFFRACTION14chain 'C' and (resid 3 through 39 )
15X-RAY DIFFRACTION15chain 'C' and (resid 40 through 236 )
16X-RAY DIFFRACTION16chain 'C' and (resid 237 through 307 )
17X-RAY DIFFRACTION17chain 'C' and (resid 308 through 382 )
18X-RAY DIFFRACTION18chain 'C' and (resid 383 through 484 )
19X-RAY DIFFRACTION19chain 'D' and (resid 2 through 39 )
20X-RAY DIFFRACTION20chain 'D' and (resid 40 through 156 )
21X-RAY DIFFRACTION21chain 'D' and (resid 157 through 289 )
22X-RAY DIFFRACTION22chain 'D' and (resid 290 through 414 )
23X-RAY DIFFRACTION23chain 'D' and (resid 415 through 434 )
24X-RAY DIFFRACTION24chain 'D' and (resid 435 through 484 )

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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